HEADER TRANSFERASE 19-JUN-16 5GHF TITLE TRANSAMINASE WITH L-ALA COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINOTRANSFERASE CLASS-III; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRANSMANINASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OCHROBACTRUM ANTHROPI (STRAIN ATCC 49188 / DSM SOURCE 3 6882 / NCTC 12168); SOURCE 4 ORGANISM_TAXID: 439375; SOURCE 5 STRAIN: ATCC 49188 / DSM 6882 / NCTC 12168; SOURCE 6 GENE: OANT_0199; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS TRANSAMINASE, PMP, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.KIM,J.PARK REVDAT 2 20-MAR-24 5GHF 1 REMARK REVDAT 1 24-MAY-17 5GHF 0 JRNL AUTH S.-W.HAN,J.KIM,H.-S.CHO,J.-S.SHIN JRNL TITL ACTIVE SITE ENGINEERING OF OMEGA-TRANSAMINASE GUIDED BY JRNL TITL 2 DOCKING ORIENTATION ANALYSIS AND VIRTUAL ACTIVITY SCREENING JRNL REF ACS CATALYSIS V. 7 3752 2017 JRNL REFN ESSN 2155-5435 JRNL DOI 10.1021/ACSCATAL.6B03242 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 58830 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) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3136 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4229 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.1390 REMARK 3 BIN FREE R VALUE SET COUNT : 228 REMARK 3 BIN FREE R VALUE : 0.1950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6554 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 956 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.142 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.128 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.746 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6695 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6501 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9071 ; 1.869 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14944 ; 1.086 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 851 ; 6.133 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 287 ;34.327 ;23.693 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1132 ;11.744 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 51 ;18.250 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1027 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7566 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1476 ; 0.002 ; 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): 3416 ; 1.137 ; 0.833 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3415 ; 1.136 ; 0.831 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4263 ; 1.779 ; 1.238 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4264 ; 1.779 ; 1.240 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3279 ; 2.431 ; 1.114 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3280 ; 2.431 ; 1.114 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4809 ; 3.804 ; 1.565 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 30638 ; 5.473 ; 8.861 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 30639 ; 5.473 ; 8.861 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 : NULL 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 REMARK 4 REMARK 4 5GHF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1300000774. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58830 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 27.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.14700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL PH 8.5, 23% PEG 3350, REMARK 280 EVAPORATION, RECRYSTALLIZATION, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 39.40000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.36500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.36500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.00000 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: 8510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 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 1 REMARK 465 THR A 2 REMARK 465 ALA A 3 REMARK 465 THR A 85 REMARK 465 PHE A 86 REMARK 465 SER A 87 REMARK 465 TYR A 88 REMARK 465 ARG A 89 REMARK 465 SER A 90 REMARK 465 HIS A 91 REMARK 465 GLU A 311 REMARK 465 GLU A 312 REMARK 465 SER A 313 REMARK 465 HIS A 314 REMARK 465 LYS A 315 REMARK 465 ILE A 316 REMARK 465 GLY A 317 REMARK 465 THR A 318 REMARK 465 LEU A 319 REMARK 465 GLY A 320 REMARK 465 THR A 321 REMARK 465 GLY A 322 REMARK 465 PHE A 323 REMARK 465 THR A 324 REMARK 465 ALA A 325 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ALA B 3 REMARK 465 GLN B 4 REMARK 465 PRO B 5 REMARK 465 ASN B 6 REMARK 465 SER B 7 REMARK 465 LEU B 8 REMARK 465 GLU B 9 REMARK 465 ALA B 10 REMARK 465 ARG B 11 REMARK 465 ASP B 12 REMARK 465 ILE B 13 REMARK 465 ARG B 14 REMARK 465 TYR B 15 REMARK 465 HIS B 16 REMARK 465 LEU B 17 REMARK 465 HIS B 18 REMARK 465 SER B 19 REMARK 465 TYR B 20 REMARK 465 THR B 21 REMARK 465 ASP B 22 REMARK 465 ALA B 23 REMARK 465 VAL B 24 REMARK 465 ARG B 25 REMARK 465 LEU B 26 REMARK 465 GLU B 27 REMARK 465 ALA B 28 REMARK 465 GLU B 29 REMARK 465 GLY B 30 REMARK 465 PRO B 31 REMARK 465 ARG B 456 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 HOH B 793 O HOH B 838 1.94 REMARK 500 O HOH A 697 O HOH A 1039 2.00 REMARK 500 O HOH B 714 O HOH B 821 2.00 REMARK 500 O HOH A 957 O HOH A 1022 2.03 REMARK 500 O HOH A 668 O HOH A 992 2.03 REMARK 500 NH2 ARG A 25 O HOH A 601 2.06 REMARK 500 O HOH B 544 O HOH B 736 2.10 REMARK 500 O HOH A 905 O HOH B 773 2.12 REMARK 500 O HOH A 681 O HOH A 741 2.15 REMARK 500 O HOH A 728 O HOH A 786 2.15 REMARK 500 NH1 ARG A 361 OD1 ASP A 437 2.17 REMARK 500 O HOH A 1064 O HOH A 1107 2.17 REMARK 500 OE2 GLU B 303 O HOH B 501 2.18 REMARK 500 O HOH B 617 O HOH B 796 2.19 REMARK 500 O HOH A 972 O HOH B 806 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 621 O HOH A 671 4545 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 SER B 119 CB SER B 119 OG -0.085 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 A 11 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 11 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP A 346 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 352 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 354 CB - CG - CD ANGL. DEV. = 18.9 DEGREES REMARK 500 ARG A 354 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 354 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 456 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 304 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 352 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 354 CB - CG - CD ANGL. DEV. = 18.1 DEGREES REMARK 500 ARG B 354 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP B 388 CB - CG - OD1 ANGL. DEV. = 6.9 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 146 -167.93 -115.89 REMARK 500 ARG A 149 -0.57 72.10 REMARK 500 SER A 170 -1.81 69.86 REMARK 500 ARG A 177 -11.15 90.50 REMARK 500 THR A 239 -7.52 83.21 REMARK 500 SER A 286 -155.89 -160.96 REMARK 500 LYS A 287 -96.91 61.97 REMARK 500 SER A 292 19.39 59.43 REMARK 500 SER A 416 -166.81 -109.08 REMARK 500 CYS A 426 65.65 -153.07 REMARK 500 LEU B 57 65.34 -116.77 REMARK 500 SER B 65 57.70 -145.41 REMARK 500 SER B 170 -0.87 78.15 REMARK 500 ARG B 177 -7.68 94.78 REMARK 500 THR B 239 -2.92 78.11 REMARK 500 SER B 286 -156.77 -159.70 REMARK 500 LYS B 287 -97.75 61.36 REMARK 500 CYS B 426 64.51 -150.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1107 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A1108 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A1109 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A1110 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A1111 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A1112 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A1113 DISTANCE = 6.82 ANGSTROMS REMARK 525 HOH A1114 DISTANCE = 6.88 ANGSTROMS REMARK 525 HOH A1115 DISTANCE = 7.34 ANGSTROMS REMARK 525 HOH A1116 DISTANCE = 7.68 ANGSTROMS REMARK 525 HOH B 940 DISTANCE = 6.26 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PMP A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GHG RELATED DB: PDB DBREF 5GHF A 1 456 UNP A6WVC6 A6WVC6_OCHA4 1 456 DBREF 5GHF B 1 456 UNP A6WVC6 A6WVC6_OCHA4 1 456 SEQRES 1 A 456 MET THR ALA GLN PRO ASN SER LEU GLU ALA ARG ASP ILE SEQRES 2 A 456 ARG TYR HIS LEU HIS SER TYR THR ASP ALA VAL ARG LEU SEQRES 3 A 456 GLU ALA GLU GLY PRO LEU VAL ILE GLU ARG GLY ASP GLY SEQRES 4 A 456 ILE TYR VAL GLU ASP VAL SER GLY LYS ARG TYR ILE GLU SEQRES 5 A 456 ALA MET SER GLY LEU TRP SER VAL GLY VAL GLY PHE SER SEQRES 6 A 456 GLU PRO ARG LEU ALA GLU ALA ALA ALA ARG GLN MET LYS SEQRES 7 A 456 LYS LEU PRO PHE TYR HIS THR PHE SER TYR ARG SER HIS SEQRES 8 A 456 GLY PRO VAL ILE ASP LEU ALA GLU LYS LEU VAL SER MET SEQRES 9 A 456 ALA PRO VAL PRO MET SER LYS ALA TYR PHE THR ASN SER SEQRES 10 A 456 GLY SER GLU ALA ASN ASP THR VAL VAL LYS LEU ILE TRP SEQRES 11 A 456 TYR ARG SER ASN ALA LEU GLY GLU PRO GLU ARG LYS LYS SEQRES 12 A 456 ILE ILE SER ARG LYS ARG GLY TYR HIS GLY VAL THR ILE SEQRES 13 A 456 ALA SER ALA SER LEU THR GLY LEU PRO ASN ASN HIS ARG SEQRES 14 A 456 SER PHE ASP LEU PRO ILE ASP ARG ILE LEU HIS THR GLY SEQRES 15 A 456 CYS PRO HIS PHE TYR ARG GLU GLY GLN ALA GLY GLU SER SEQRES 16 A 456 GLU GLU GLN PHE ALA THR ARG LEU ALA ASP GLU LEU GLU SEQRES 17 A 456 GLN LEU ILE ILE ALA GLU GLY PRO HIS THR ILE ALA ALA SEQRES 18 A 456 PHE ILE GLY GLU PRO VAL MET GLY ALA GLY GLY VAL VAL SEQRES 19 A 456 VAL PRO PRO LYS THR TYR TRP GLU LYS VAL GLN ALA VAL SEQRES 20 A 456 LEU LYS ARG TYR ASP ILE LEU LEU ILE ALA ASP GLU VAL SEQRES 21 A 456 ILE CYS GLY PHE GLY ARG THR GLY ASN LEU PHE GLY SER SEQRES 22 A 456 GLN THR PHE ASP MET LYS PRO ASP ILE LEU VAL MET SER SEQRES 23 A 456 LYS GLN LEU SER SER SER TYR LEU PRO ILE SER ALA PHE SEQRES 24 A 456 LEU ILE ASN GLU ARG VAL TYR ALA PRO ILE ALA GLU GLU SEQRES 25 A 456 SER HIS LYS ILE GLY THR LEU GLY THR GLY PHE THR ALA SEQRES 26 A 456 SER GLY HIS PRO VAL ALA ALA ALA VAL ALA LEU GLU ASN SEQRES 27 A 456 LEU ALA ILE ILE GLU GLU ARG ASP LEU VAL ALA ASN ALA SEQRES 28 A 456 ARG ASP ARG GLY THR TYR MET GLN LYS ARG LEU ARG GLU SEQRES 29 A 456 LEU GLN ASP HIS PRO LEU VAL GLY GLU VAL ARG GLY VAL SEQRES 30 A 456 GLY LEU ILE ALA GLY VAL GLU LEU VAL THR ASP LYS GLN SEQRES 31 A 456 ALA LYS THR GLY LEU GLU PRO THR GLY ALA LEU GLY ALA SEQRES 32 A 456 LYS ALA ASN ALA VAL LEU GLN GLU ARG GLY VAL ILE SER SEQRES 33 A 456 ARG ALA MET GLY ASP THR LEU ALA PHE CYS PRO PRO LEU SEQRES 34 A 456 ILE ILE ASN ASP GLN GLN VAL ASP THR MET VAL SER ALA SEQRES 35 A 456 LEU GLU ALA THR LEU ASN ASP VAL GLN ALA SER LEU THR SEQRES 36 A 456 ARG SEQRES 1 B 456 MET THR ALA GLN PRO ASN SER LEU GLU ALA ARG ASP ILE SEQRES 2 B 456 ARG TYR HIS LEU HIS SER TYR THR ASP ALA VAL ARG LEU SEQRES 3 B 456 GLU ALA GLU GLY PRO LEU VAL ILE GLU ARG GLY ASP GLY SEQRES 4 B 456 ILE TYR VAL GLU ASP VAL SER GLY LYS ARG TYR ILE GLU SEQRES 5 B 456 ALA MET SER GLY LEU TRP SER VAL GLY VAL GLY PHE SER SEQRES 6 B 456 GLU PRO ARG LEU ALA GLU ALA ALA ALA ARG GLN MET LYS SEQRES 7 B 456 LYS LEU PRO PHE TYR HIS THR PHE SER TYR ARG SER HIS SEQRES 8 B 456 GLY PRO VAL ILE ASP LEU ALA GLU LYS LEU VAL SER MET SEQRES 9 B 456 ALA PRO VAL PRO MET SER LYS ALA TYR PHE THR ASN SER SEQRES 10 B 456 GLY SER GLU ALA ASN ASP THR VAL VAL LYS LEU ILE TRP SEQRES 11 B 456 TYR ARG SER ASN ALA LEU GLY GLU PRO GLU ARG LYS LYS SEQRES 12 B 456 ILE ILE SER ARG LYS ARG GLY TYR HIS GLY VAL THR ILE SEQRES 13 B 456 ALA SER ALA SER LEU THR GLY LEU PRO ASN ASN HIS ARG SEQRES 14 B 456 SER PHE ASP LEU PRO ILE ASP ARG ILE LEU HIS THR GLY SEQRES 15 B 456 CYS PRO HIS PHE TYR ARG GLU GLY GLN ALA GLY GLU SER SEQRES 16 B 456 GLU GLU GLN PHE ALA THR ARG LEU ALA ASP GLU LEU GLU SEQRES 17 B 456 GLN LEU ILE ILE ALA GLU GLY PRO HIS THR ILE ALA ALA SEQRES 18 B 456 PHE ILE GLY GLU PRO VAL MET GLY ALA GLY GLY VAL VAL SEQRES 19 B 456 VAL PRO PRO LYS THR TYR TRP GLU LYS VAL GLN ALA VAL SEQRES 20 B 456 LEU LYS ARG TYR ASP ILE LEU LEU ILE ALA ASP GLU VAL SEQRES 21 B 456 ILE CYS GLY PHE GLY ARG THR GLY ASN LEU PHE GLY SER SEQRES 22 B 456 GLN THR PHE ASP MET LYS PRO ASP ILE LEU VAL MET SER SEQRES 23 B 456 LYS GLN LEU SER SER SER TYR LEU PRO ILE SER ALA PHE SEQRES 24 B 456 LEU ILE ASN GLU ARG VAL TYR ALA PRO ILE ALA GLU GLU SEQRES 25 B 456 SER HIS LYS ILE GLY THR LEU GLY THR GLY PHE THR ALA SEQRES 26 B 456 SER GLY HIS PRO VAL ALA ALA ALA VAL ALA LEU GLU ASN SEQRES 27 B 456 LEU ALA ILE ILE GLU GLU ARG ASP LEU VAL ALA ASN ALA SEQRES 28 B 456 ARG ASP ARG GLY THR TYR MET GLN LYS ARG LEU ARG GLU SEQRES 29 B 456 LEU GLN ASP HIS PRO LEU VAL GLY GLU VAL ARG GLY VAL SEQRES 30 B 456 GLY LEU ILE ALA GLY VAL GLU LEU VAL THR ASP LYS GLN SEQRES 31 B 456 ALA LYS THR GLY LEU GLU PRO THR GLY ALA LEU GLY ALA SEQRES 32 B 456 LYS ALA ASN ALA VAL LEU GLN GLU ARG GLY VAL ILE SER SEQRES 33 B 456 ARG ALA MET GLY ASP THR LEU ALA PHE CYS PRO PRO LEU SEQRES 34 B 456 ILE ILE ASN ASP GLN GLN VAL ASP THR MET VAL SER ALA SEQRES 35 B 456 LEU GLU ALA THR LEU ASN ASP VAL GLN ALA SER LEU THR SEQRES 36 B 456 ARG HET PMP A 501 16 HETNAM PMP 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE HETSYN PMP PYRIDOXAMINE-5'-PHOSPHATE FORMUL 3 PMP C8 H13 N2 O5 P FORMUL 4 HOH *956(H2 O) HELIX 1 AA1 SER A 7 HIS A 16 1 10 HELIX 2 AA2 ASP A 22 GLY A 30 1 9 HELIX 3 AA3 MET A 54 SER A 59 1 6 HELIX 4 AA4 GLU A 66 LYS A 78 1 13 HELIX 5 AA5 PRO A 93 ALA A 105 1 13 HELIX 6 AA6 SER A 117 LEU A 136 1 20 HELIX 7 AA7 THR A 155 THR A 162 1 8 HELIX 8 AA8 LEU A 164 HIS A 168 5 5 HELIX 9 AA9 HIS A 185 GLY A 190 1 6 HELIX 10 AB1 SER A 195 GLY A 215 1 21 HELIX 11 AB2 THR A 239 TYR A 251 1 13 HELIX 12 AB3 PHE A 271 PHE A 276 1 6 HELIX 13 AB4 SER A 286 SER A 290 5 5 HELIX 14 AB5 ASN A 302 ALA A 307 1 6 HELIX 15 AB6 PRO A 308 ALA A 310 5 3 HELIX 16 AB7 HIS A 328 ARG A 345 1 18 HELIX 17 AB8 ASP A 346 GLU A 364 1 19 HELIX 18 AB9 GLY A 399 ARG A 412 1 14 HELIX 19 AC1 ASN A 432 ARG A 456 1 25 HELIX 20 AC2 MET B 54 SER B 59 1 6 HELIX 21 AC3 GLU B 66 LEU B 80 1 15 HELIX 22 AC4 GLY B 92 MET B 104 1 13 HELIX 23 AC5 SER B 117 LEU B 136 1 20 HELIX 24 AC6 THR B 155 THR B 162 1 8 HELIX 25 AC7 LEU B 164 HIS B 168 5 5 HELIX 26 AC8 HIS B 185 GLY B 190 1 6 HELIX 27 AC9 SER B 195 GLY B 215 1 21 HELIX 28 AD1 THR B 239 ASP B 252 1 14 HELIX 29 AD2 PHE B 271 PHE B 276 1 6 HELIX 30 AD3 SER B 286 SER B 290 5 5 HELIX 31 AD4 ASN B 302 GLY B 317 1 16 HELIX 32 AD5 HIS B 328 ARG B 345 1 18 HELIX 33 AD6 ASP B 346 GLU B 364 1 19 HELIX 34 AD7 GLY B 399 ARG B 412 1 14 HELIX 35 AD8 ASN B 432 THR B 455 1 24 SHEET 1 AA1 5 VAL A 414 ILE A 415 0 SHEET 2 AA1 5 ARG A 49 GLU A 52 1 N ILE A 51 O ILE A 415 SHEET 3 AA1 5 TYR A 41 ASP A 44 -1 N VAL A 42 O TYR A 50 SHEET 4 AA1 5 LEU A 32 ASP A 38 -1 N ARG A 36 O GLU A 43 SHEET 5 AA1 5 ARG B 89 HIS B 91 1 O SER B 90 N ILE A 34 SHEET 1 AA2 7 LYS A 111 THR A 115 0 SHEET 2 AA2 7 SER A 297 ILE A 301 -1 O SER A 297 N THR A 115 SHEET 3 AA2 7 ILE A 282 MET A 285 -1 N MET A 285 O ALA A 298 SHEET 4 AA2 7 LEU A 254 ASP A 258 1 N ALA A 257 O ILE A 282 SHEET 5 AA2 7 ILE A 219 GLY A 224 1 N PHE A 222 O LEU A 254 SHEET 6 AA2 7 LYS A 143 ARG A 147 1 N LYS A 143 O ALA A 220 SHEET 7 AA2 7 ILE A 178 THR A 181 1 O LEU A 179 N ILE A 144 SHEET 1 AA3 4 VAL A 371 VAL A 377 0 SHEET 2 AA3 4 ILE A 380 LEU A 385 -1 O GLY A 382 N ARG A 375 SHEET 3 AA3 4 THR A 422 PHE A 425 -1 O LEU A 423 N VAL A 383 SHEET 4 AA3 4 ARG A 417 MET A 419 -1 N MET A 419 O THR A 422 SHEET 1 AA4 4 ILE B 34 ASP B 38 0 SHEET 2 AA4 4 TYR B 41 ASP B 44 -1 O GLU B 43 N ARG B 36 SHEET 3 AA4 4 ARG B 49 GLU B 52 -1 O TYR B 50 N VAL B 42 SHEET 4 AA4 4 VAL B 414 ILE B 415 1 O ILE B 415 N ILE B 51 SHEET 1 AA5 7 LYS B 111 THR B 115 0 SHEET 2 AA5 7 SER B 297 ILE B 301 -1 O SER B 297 N THR B 115 SHEET 3 AA5 7 ILE B 282 MET B 285 -1 N MET B 285 O ALA B 298 SHEET 4 AA5 7 LEU B 254 ASP B 258 1 N ALA B 257 O ILE B 282 SHEET 5 AA5 7 ILE B 219 GLY B 224 1 N PHE B 222 O ILE B 256 SHEET 6 AA5 7 LYS B 143 ARG B 147 1 N ILE B 145 O ALA B 221 SHEET 7 AA5 7 ILE B 178 THR B 181 1 O LEU B 179 N SER B 146 SHEET 1 AA6 4 VAL B 371 VAL B 377 0 SHEET 2 AA6 4 ILE B 380 LEU B 385 -1 O GLY B 382 N ARG B 375 SHEET 3 AA6 4 THR B 422 PHE B 425 -1 O PHE B 425 N ALA B 381 SHEET 4 AA6 4 ARG B 417 MET B 419 -1 N MET B 419 O THR B 422 CISPEP 1 LEU A 173 PRO A 174 0 -0.31 CISPEP 2 GLU A 396 PRO A 397 0 -13.00 CISPEP 3 LEU B 173 PRO B 174 0 5.35 CISPEP 4 GLU B 396 PRO B 397 0 -17.72 SITE 1 AC1 16 SER A 117 GLY A 118 SER A 119 TYR A 151 SITE 2 AC1 16 HIS A 152 GLU A 225 ASP A 258 VAL A 260 SITE 3 AC1 16 ILE A 261 LYS A 287 HOH A 612 HOH A 636 SITE 4 AC1 16 HOH A 655 HOH A 724 HOH A 757 THR B 324 CRYST1 78.800 102.000 116.730 90.00 90.00 90.00 P 21 21 21 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 0.012690 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009804 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008567 0.00000