HEADER TRANSFERASE/TRANSFERASE INHIBITOR 10-DEC-14 4RXE TITLE T. BRUCEI FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH BISPHOSPHONATE TITLE 2 BPH-14 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FARNESYL PYROPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.CAO,Y.-L.LIU,E.OLDFIELD REVDAT 2 20-SEP-23 4RXE 1 REMARK SEQADV LINK REVDAT 1 15-APR-15 4RXE 0 JRNL AUTH Y.L.LIU,R.CAO,Y.WANG,E.OLDFIELD JRNL TITL FARNESYL DIPHOSPHATE SYNTHASE INHIBITORS WITH UNIQUE JRNL TITL 2 LIGAND-BINDING GEOMETRIES. JRNL REF ACS MED CHEM LETT V. 6 349 2015 JRNL REFN ISSN 1948-5875 JRNL PMID 25815158 JRNL DOI 10.1021/ML500528X REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 28806 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1537 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2162 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5736 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.44000 REMARK 3 B22 (A**2) : -2.90000 REMARK 3 B33 (A**2) : 0.45000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.551 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.299 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.203 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.967 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5888 ; 0.015 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 5554 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7971 ; 1.826 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12771 ; 0.915 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 713 ; 6.245 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 271 ;37.346 ;23.948 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1037 ;17.796 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;17.010 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 887 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6577 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1343 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2864 ; 3.640 ; 4.721 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2863 ; 3.635 ; 4.719 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3573 ; 5.269 ; 7.062 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4RXE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000087914. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 5.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 2OGD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% MPD, 0.1 AMMONIUM ACETATE, PH REMARK 280 5.75, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 67.07450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.57450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.07450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 59.57450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -98.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -22 REMARK 465 GLY A -21 REMARK 465 SER A -20 REMARK 465 SER A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 SER A -12 REMARK 465 SER A -11 REMARK 465 GLY A -10 REMARK 465 LEU A -9 REMARK 465 VAL A -8 REMARK 465 PRO A -7 REMARK 465 ARG A -6 REMARK 465 GLY A -5 REMARK 465 SER A -4 REMARK 465 HIS A -3 REMARK 465 MET A -2 REMARK 465 ALA A -1 REMARK 465 SER A 0 REMARK 465 SER A 65 REMARK 465 PRO A 66 REMARK 465 ASN A 67 REMARK 465 ASN A 68 REMARK 465 ASN A 69 REMARK 465 GLY A 70 REMARK 465 GLU A 71 REMARK 465 GLU A 72 REMARK 465 ASP A 73 REMARK 465 MET B -22 REMARK 465 GLY B -21 REMARK 465 SER B -20 REMARK 465 SER B -19 REMARK 465 HIS B -18 REMARK 465 HIS B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 SER B -12 REMARK 465 SER B -11 REMARK 465 GLY B -10 REMARK 465 LEU B -9 REMARK 465 VAL B -8 REMARK 465 PRO B -7 REMARK 465 ARG B -6 REMARK 465 GLY B -5 REMARK 465 SER B -4 REMARK 465 HIS B -3 REMARK 465 MET B -2 REMARK 465 ALA B -1 REMARK 465 SER B 0 REMARK 465 SER B 65 REMARK 465 PRO B 66 REMARK 465 ASN B 67 REMARK 465 ASN B 68 REMARK 465 ASN B 69 REMARK 465 GLY B 70 REMARK 465 GLU B 71 REMARK 465 GLU B 72 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 123 CG OD1 OD2 REMARK 470 GLN A 191 CG CD OE1 NE2 REMARK 470 ASP B 123 CG OD1 OD2 REMARK 470 GLU B 265 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASP A 186 CB ASP B 123 2.01 REMARK 500 O LYS B 278 OH TYR B 302 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 36 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 50 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP B 107 CB - CG - OD1 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG B 112 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 112 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 60 2.18 -66.13 REMARK 500 ALA A 76 -2.43 -142.22 REMARK 500 CYS A 117 156.57 -47.81 REMARK 500 GLN A 191 126.97 -171.16 REMARK 500 PRO A 264 -37.94 -31.39 REMARK 500 ASP A 321 46.19 70.20 REMARK 500 GLN A 366 -64.59 -99.96 REMARK 500 ASP B 181 109.49 -34.96 REMARK 500 ASP B 186 116.12 -168.02 REMARK 500 SER B 190 152.86 -46.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A3002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 OD2 REMARK 620 2 ASP A 107 OD2 74.3 REMARK 620 3 3YQ A3001 O5 82.9 117.0 REMARK 620 4 3YQ A3001 O4 66.4 53.4 63.7 REMARK 620 5 HOH A3166 O 130.3 70.4 83.1 64.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A3004 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 OD1 REMARK 620 2 ASP A 107 OD2 78.4 REMARK 620 3 ASP A 107 OD1 87.2 49.8 REMARK 620 4 3YQ A3001 O4 93.1 62.5 110.7 REMARK 620 5 HOH A3164 O 153.8 75.6 74.0 77.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A3003 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 255 OD2 REMARK 620 2 3YQ A3001 O3 104.0 REMARK 620 3 3YQ A3001 O6 84.8 70.1 REMARK 620 4 HOH A3130 O 96.4 145.0 84.1 REMARK 620 5 HOH A3165 O 160.9 75.4 77.0 76.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B4002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 103 OD2 REMARK 620 2 ASP B 107 OD2 81.1 REMARK 620 3 3YQ B4001 O2 80.9 130.8 REMARK 620 4 3YQ B4001 O4 73.0 61.9 69.1 REMARK 620 5 HOH B4191 O 154.2 81.7 96.2 82.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B4004 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 103 OD1 REMARK 620 2 ASP B 107 OD2 69.5 REMARK 620 3 3YQ B4001 O4 95.0 65.4 REMARK 620 4 HOH B4192 O 69.2 74.4 139.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B4003 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 255 OD2 REMARK 620 2 3YQ B4001 O1 85.4 REMARK 620 3 3YQ B4001 O5 72.7 70.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3YQ A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 3002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 3003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 3004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3YQ B 4001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 4002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 4003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 4004 DBREF 4RXE A 1 367 UNP Q86C09 Q86C09_9TRYP 1 367 DBREF 4RXE B 1 367 UNP Q86C09 Q86C09_9TRYP 1 367 SEQADV 4RXE MET A -22 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE GLY A -21 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE SER A -20 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE SER A -19 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE HIS A -18 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE HIS A -17 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE HIS A -16 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE HIS A -15 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE HIS A -14 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE HIS A -13 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE SER A -12 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE SER A -11 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE GLY A -10 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE LEU A -9 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE VAL A -8 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE PRO A -7 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE ARG A -6 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE GLY A -5 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE SER A -4 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE HIS A -3 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE MET A -2 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE ALA A -1 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE SER A 0 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE MET B -22 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE GLY B -21 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE SER B -20 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE SER B -19 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE HIS B -18 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE HIS B -17 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE HIS B -16 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE HIS B -15 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE HIS B -14 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE HIS B -13 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE SER B -12 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE SER B -11 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE GLY B -10 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE LEU B -9 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE VAL B -8 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE PRO B -7 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE ARG B -6 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE GLY B -5 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE SER B -4 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE HIS B -3 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE MET B -2 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE ALA B -1 UNP Q86C09 EXPRESSION TAG SEQADV 4RXE SER B 0 UNP Q86C09 EXPRESSION TAG SEQRES 1 A 390 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 390 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET PRO MET SEQRES 3 A 390 GLN MET PHE MET GLN VAL TYR ASP GLU ILE GLN MET PHE SEQRES 4 A 390 LEU LEU GLU GLU LEU GLU LEU LYS PHE ASP MET ASP PRO SEQRES 5 A 390 ASN ARG VAL ARG TYR LEU ARG LYS MET MET ASP THR THR SEQRES 6 A 390 CYS LEU GLY GLY LYS TYR ASN ARG GLY LEU THR VAL ILE SEQRES 7 A 390 ASP VAL ALA GLU SER LEU LEU SER LEU SER PRO ASN ASN SEQRES 8 A 390 ASN GLY GLU GLU ASP ASP GLY ALA ARG ARG LYS ARG VAL SEQRES 9 A 390 LEU HIS ASP ALA CYS VAL CYS GLY TRP MET ILE GLU PHE SEQRES 10 A 390 LEU GLN ALA HIS TYR LEU VAL GLU ASP ASP ILE MET ASP SEQRES 11 A 390 ASN SER VAL THR ARG ARG GLY LYS PRO CYS TRP TYR ARG SEQRES 12 A 390 HIS PRO ASP VAL THR VAL GLN CYS ALA ILE ASN ASP GLY SEQRES 13 A 390 LEU LEU LEU LYS SER TRP THR HIS MET MET ALA MET HIS SEQRES 14 A 390 PHE PHE ALA ASP ARG PRO PHE LEU GLN ASP LEU LEU CYS SEQRES 15 A 390 ARG PHE ASN ARG VAL ASP TYR THR THR ALA VAL GLY GLN SEQRES 16 A 390 LEU TYR ASP VAL THR SER MET PHE ASP SER ASN LYS LEU SEQRES 17 A 390 ASP PRO ASP VAL SER GLN PRO THR THR THR ASP PHE ALA SEQRES 18 A 390 GLU PHE THR LEU SER ASN TYR LYS ARG ILE VAL LYS TYR SEQRES 19 A 390 LYS THR ALA TYR TYR THR TYR LEU LEU PRO LEU VAL MET SEQRES 20 A 390 GLY LEU ILE VAL SER GLU ALA LEU PRO THR VAL ASP MET SEQRES 21 A 390 GLY VAL THR GLU GLU LEU ALA MET LEU MET GLY GLU TYR SEQRES 22 A 390 PHE GLN VAL GLN ASP ASP VAL MET ASP CYS PHE THR PRO SEQRES 23 A 390 PRO GLU ARG LEU GLY LYS VAL GLY THR ASP ILE GLN ASP SEQRES 24 A 390 ALA LYS CYS SER TRP LEU ALA VAL THR PHE LEU ALA LYS SEQRES 25 A 390 ALA SER SER ALA GLN VAL ALA GLU PHE LYS ALA ASN TYR SEQRES 26 A 390 GLY SER GLY ASP SER GLU LYS VAL ALA THR VAL ARG ARG SEQRES 27 A 390 LEU TYR GLU GLU ALA ASP LEU GLN GLY ASP TYR VAL ALA SEQRES 28 A 390 TYR GLU ALA ALA VAL ALA GLU GLN VAL LYS GLU LEU ILE SEQRES 29 A 390 GLU LYS LEU ARG LEU CYS SER PRO GLY PHE ALA ALA SER SEQRES 30 A 390 VAL GLU THR LEU TRP GLY LYS THR TYR LYS ARG GLN LYS SEQRES 1 B 390 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 390 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET PRO MET SEQRES 3 B 390 GLN MET PHE MET GLN VAL TYR ASP GLU ILE GLN MET PHE SEQRES 4 B 390 LEU LEU GLU GLU LEU GLU LEU LYS PHE ASP MET ASP PRO SEQRES 5 B 390 ASN ARG VAL ARG TYR LEU ARG LYS MET MET ASP THR THR SEQRES 6 B 390 CYS LEU GLY GLY LYS TYR ASN ARG GLY LEU THR VAL ILE SEQRES 7 B 390 ASP VAL ALA GLU SER LEU LEU SER LEU SER PRO ASN ASN SEQRES 8 B 390 ASN GLY GLU GLU ASP ASP GLY ALA ARG ARG LYS ARG VAL SEQRES 9 B 390 LEU HIS ASP ALA CYS VAL CYS GLY TRP MET ILE GLU PHE SEQRES 10 B 390 LEU GLN ALA HIS TYR LEU VAL GLU ASP ASP ILE MET ASP SEQRES 11 B 390 ASN SER VAL THR ARG ARG GLY LYS PRO CYS TRP TYR ARG SEQRES 12 B 390 HIS PRO ASP VAL THR VAL GLN CYS ALA ILE ASN ASP GLY SEQRES 13 B 390 LEU LEU LEU LYS SER TRP THR HIS MET MET ALA MET HIS SEQRES 14 B 390 PHE PHE ALA ASP ARG PRO PHE LEU GLN ASP LEU LEU CYS SEQRES 15 B 390 ARG PHE ASN ARG VAL ASP TYR THR THR ALA VAL GLY GLN SEQRES 16 B 390 LEU TYR ASP VAL THR SER MET PHE ASP SER ASN LYS LEU SEQRES 17 B 390 ASP PRO ASP VAL SER GLN PRO THR THR THR ASP PHE ALA SEQRES 18 B 390 GLU PHE THR LEU SER ASN TYR LYS ARG ILE VAL LYS TYR SEQRES 19 B 390 LYS THR ALA TYR TYR THR TYR LEU LEU PRO LEU VAL MET SEQRES 20 B 390 GLY LEU ILE VAL SER GLU ALA LEU PRO THR VAL ASP MET SEQRES 21 B 390 GLY VAL THR GLU GLU LEU ALA MET LEU MET GLY GLU TYR SEQRES 22 B 390 PHE GLN VAL GLN ASP ASP VAL MET ASP CYS PHE THR PRO SEQRES 23 B 390 PRO GLU ARG LEU GLY LYS VAL GLY THR ASP ILE GLN ASP SEQRES 24 B 390 ALA LYS CYS SER TRP LEU ALA VAL THR PHE LEU ALA LYS SEQRES 25 B 390 ALA SER SER ALA GLN VAL ALA GLU PHE LYS ALA ASN TYR SEQRES 26 B 390 GLY SER GLY ASP SER GLU LYS VAL ALA THR VAL ARG ARG SEQRES 27 B 390 LEU TYR GLU GLU ALA ASP LEU GLN GLY ASP TYR VAL ALA SEQRES 28 B 390 TYR GLU ALA ALA VAL ALA GLU GLN VAL LYS GLU LEU ILE SEQRES 29 B 390 GLU LYS LEU ARG LEU CYS SER PRO GLY PHE ALA ALA SER SEQRES 30 B 390 VAL GLU THR LEU TRP GLY LYS THR TYR LYS ARG GLN LYS HET 3YQ A3001 17 HET MG A3002 1 HET MG A3003 1 HET MG A3004 1 HET 3YQ B4001 17 HET MG B4002 1 HET MG B4003 1 HET MG B4004 1 HETNAM 3YQ {[(3-METHYLPYRIDIN-2-YL) HETNAM 2 3YQ AMINO]METHANEDIYL}BIS(PHOSPHONIC ACID) HETNAM MG MAGNESIUM ION FORMUL 3 3YQ 2(C7 H12 N2 O6 P2) FORMUL 4 MG 6(MG 2+) FORMUL 11 HOH *158(H2 O) HELIX 1 1 MET A 1 PHE A 25 1 25 HELIX 2 2 ASP A 28 LEU A 44 1 17 HELIX 3 3 TYR A 48 SER A 60 1 13 HELIX 4 4 ALA A 76 ASP A 107 1 32 HELIX 5 5 TRP A 118 HIS A 121 5 4 HELIX 6 6 THR A 125 ALA A 149 1 25 HELIX 7 7 PHE A 153 THR A 177 1 25 HELIX 8 8 ASP A 181 LEU A 185 5 5 HELIX 9 9 THR A 201 THR A 213 1 13 HELIX 10 10 THR A 213 TYR A 218 1 6 HELIX 11 11 TYR A 218 GLU A 230 1 13 HELIX 12 12 ALA A 231 VAL A 235 5 5 HELIX 13 13 ASP A 236 THR A 262 1 27 HELIX 14 14 PRO A 263 GLY A 268 1 6 HELIX 15 15 SER A 280 ALA A 290 1 11 HELIX 16 16 SER A 291 ALA A 300 1 10 HELIX 17 17 ASP A 306 GLU A 319 1 14 HELIX 18 18 ASP A 321 SER A 348 1 28 HELIX 19 19 SER A 348 LYS A 361 1 14 HELIX 20 20 PRO B 2 PHE B 25 1 24 HELIX 21 21 ASP B 28 LEU B 44 1 17 HELIX 22 22 TYR B 48 LEU B 62 1 15 HELIX 23 23 GLY B 75 ASN B 108 1 34 HELIX 24 24 TRP B 118 HIS B 121 5 4 HELIX 25 25 THR B 125 ALA B 149 1 25 HELIX 26 26 PHE B 153 THR B 177 1 25 HELIX 27 27 ASP B 181 LEU B 185 5 5 HELIX 28 28 THR B 201 THR B 213 1 13 HELIX 29 29 THR B 213 TYR B 218 1 6 HELIX 30 30 TYR B 218 SER B 229 1 12 HELIX 31 31 GLU B 230 VAL B 235 5 6 HELIX 32 32 ASP B 236 THR B 262 1 27 HELIX 33 33 PRO B 263 GLY B 268 1 6 HELIX 34 34 SER B 280 ALA B 290 1 11 HELIX 35 35 SER B 291 TYR B 302 1 12 HELIX 36 36 ASP B 306 ALA B 320 1 15 HELIX 37 37 ASP B 321 LEU B 346 1 26 HELIX 38 38 SER B 348 LYS B 361 1 14 SHEET 1 A 2 THR A 111 ARG A 112 0 SHEET 2 A 2 LYS A 115 PRO A 116 -1 O LYS A 115 N ARG A 112 SHEET 1 B 2 THR B 111 ARG B 112 0 SHEET 2 B 2 LYS B 115 PRO B 116 -1 O LYS B 115 N ARG B 112 LINK OD2 ASP A 103 MG MG A3002 1555 1555 2.21 LINK OD1 ASP A 103 MG MG A3004 1555 1555 2.06 LINK OD2 ASP A 107 MG MG A3002 1555 1555 2.36 LINK OD2 ASP A 107 MG MG A3004 1555 1555 2.28 LINK OD1 ASP A 107 MG MG A3004 1555 1555 2.83 LINK OD2 ASP A 255 MG MG A3003 1555 1555 2.09 LINK O5 3YQ A3001 MG MG A3002 1555 1555 2.10 LINK O4 3YQ A3001 MG MG A3002 1555 1555 2.91 LINK O3 3YQ A3001 MG MG A3003 1555 1555 2.31 LINK O6 3YQ A3001 MG MG A3003 1555 1555 2.39 LINK O4 3YQ A3001 MG MG A3004 1555 1555 2.38 LINK MG MG A3002 O HOH A3166 1555 1555 2.25 LINK MG MG A3003 O HOH A3130 1555 1555 2.20 LINK MG MG A3003 O HOH A3165 1555 1555 2.17 LINK MG MG A3004 O HOH A3164 1555 1555 2.09 LINK OD2 ASP B 103 MG MG B4002 1555 1555 2.34 LINK OD1 ASP B 103 MG MG B4004 1555 1555 2.27 LINK OD2 ASP B 107 MG MG B4002 1555 1555 2.38 LINK OD2 ASP B 107 MG MG B4004 1555 1555 2.48 LINK OD2 ASP B 255 MG MG B4003 1555 1555 2.59 LINK O2 3YQ B4001 MG MG B4002 1555 1555 2.10 LINK O4 3YQ B4001 MG MG B4002 1555 1555 2.56 LINK O1 3YQ B4001 MG MG B4003 1555 1555 2.15 LINK O5 3YQ B4001 MG MG B4003 1555 1555 2.35 LINK O4 3YQ B4001 MG MG B4004 1555 1555 2.23 LINK MG MG B4002 O HOH B4191 1555 1555 1.88 LINK MG MG B4004 O HOH B4192 1555 1555 2.17 SITE 1 AC1 15 ASP A 103 ASP A 107 ARG A 112 LYS A 212 SITE 2 AC1 15 THR A 213 TYR A 216 ASP A 255 LYS A 269 SITE 3 AC1 15 MG A3002 MG A3003 MG A3004 HOH A3130 SITE 4 AC1 15 HOH A3164 HOH A3165 HOH A3166 SITE 1 AC2 6 ASP A 103 ASP A 104 ASP A 107 SER A 109 SITE 2 AC2 6 3YQ A3001 HOH A3166 SITE 1 AC3 5 ASP A 255 ASP A 273 3YQ A3001 HOH A3130 SITE 2 AC3 5 HOH A3165 SITE 1 AC4 5 ASP A 103 ASP A 107 ASP A 175 3YQ A3001 SITE 2 AC4 5 HOH A3164 SITE 1 AC5 14 LEU B 100 ASP B 103 ASP B 107 ARG B 112 SITE 2 AC5 14 LYS B 212 THR B 213 TYR B 216 ASP B 255 SITE 3 AC5 14 LYS B 269 MG B4002 MG B4003 MG B4004 SITE 4 AC5 14 HOH B4184 HOH B4191 SITE 1 AC6 5 ASP B 103 ASP B 107 SER B 109 3YQ B4001 SITE 2 AC6 5 HOH B4191 SITE 1 AC7 4 ASP B 255 ASP B 259 ASP B 273 3YQ B4001 SITE 1 AC8 4 ASP B 103 ASP B 107 3YQ B4001 HOH B4192 CRYST1 134.149 119.149 62.824 90.00 112.24 90.00 C 1 2 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007454 0.000000 0.003048 0.00000 SCALE2 0.000000 0.008393 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017197 0.00000