HEADER TRANSFERASE/TRANSFERASE INHIBITOR 14-SEP-10 3OTX TITLE CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI RHODESIENSE ADENOSINE KINASE TITLE 2 COMPLEXED WITH INHIBITOR AP5A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENOSINE KINASE, PUTATIVE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.1.20; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 STRAIN: RHODESIENSE; SOURCE 5 GENE: TB927.6.2360; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET30B KEYWDS ADENOSINE KINASE, AP5A, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.KUETTEL,J.GREENWALD,D.KOSTREWA,S.AHMED,L.SCAPOZZA,R.PEROZZO REVDAT 3 30-OCT-24 3OTX 1 REMARK REVDAT 2 01-NOV-23 3OTX 1 REMARK SEQADV LINK REVDAT 1 29-JUN-11 3OTX 0 JRNL AUTH S.KUETTEL,J.GREENWALD,D.KOSTREWA,S.AHMED,L.SCAPOZZA, JRNL AUTH 2 R.PEROZZO JRNL TITL CRYSTAL STRUCTURES OF T. B. RHODESIENSE ADENOSINE KINASE JRNL TITL 2 COMPLEXED WITH INHIBITOR AND ACTIVATOR: IMPLICATIONS FOR JRNL TITL 3 CATALYSIS AND HYPERACTIVATION JRNL REF PLOS NEGL TROP DIS V. 5 E1164 2011 JRNL REFN ISSN 1935-2727 JRNL PMID 21629723 JRNL DOI 10.1371/JOURNAL.PNTD.0001164 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 72.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 92189 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4858 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6689 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 324 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5253 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 116 REMARK 3 SOLVENT ATOMS : 626 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37000 REMARK 3 B22 (A**2) : -0.15000 REMARK 3 B33 (A**2) : -0.20000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.57000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.863 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5558 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7570 ; 1.485 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 703 ; 5.524 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 249 ;34.614 ;23.695 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 926 ;13.084 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;15.878 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 844 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4187 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3414 ; 1.747 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5514 ; 3.148 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2144 ; 4.642 ; 4.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2042 ; 7.160 ; 1.000 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 345 REMARK 3 RESIDUE RANGE : A 346 A 346 REMARK 3 ORIGIN FOR THE GROUP (A): 16.4990 0.2410 29.5350 REMARK 3 T TENSOR REMARK 3 T11: 0.0195 T22: 0.0126 REMARK 3 T33: 0.0228 T12: 0.0019 REMARK 3 T13: -0.0116 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 1.4449 L22: 1.0899 REMARK 3 L33: 1.2072 L12: -0.1717 REMARK 3 L13: -0.3570 L23: 0.1430 REMARK 3 S TENSOR REMARK 3 S11: 0.0008 S12: 0.0649 S13: 0.0363 REMARK 3 S21: -0.0855 S22: -0.0435 S23: -0.0531 REMARK 3 S31: -0.0321 S32: 0.0771 S33: 0.0426 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4 B 345 REMARK 3 RESIDUE RANGE : B 346 B 346 REMARK 3 ORIGIN FOR THE GROUP (A): 51.3440 7.3960 7.5320 REMARK 3 T TENSOR REMARK 3 T11: 0.0523 T22: 0.0810 REMARK 3 T33: 0.0209 T12: 0.0070 REMARK 3 T13: 0.0152 T23: 0.0090 REMARK 3 L TENSOR REMARK 3 L11: 1.3164 L22: 1.1157 REMARK 3 L33: 1.1599 L12: 0.0822 REMARK 3 L13: 0.1128 L23: 0.2437 REMARK 3 S TENSOR REMARK 3 S11: -0.0091 S12: 0.2116 S13: 0.0159 REMARK 3 S21: -0.1045 S22: -0.0204 S23: -0.0273 REMARK 3 S31: -0.0469 S32: -0.0862 S33: 0.0295 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 REMARK 4 REMARK 4 3OTX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000061568. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 97047 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 80.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43400 REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1BX4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE, 20% ISO-PROPANOL, REMARK 280 20% PEG 4000, PH 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 35.27450 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 GLY A 334 REMARK 465 CYS A 335 REMARK 465 SER A 336 REMARK 465 PHE A 337 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 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 A 373 O HOH A 636 2.04 REMARK 500 O HOH A 553 O HOH A 605 2.17 REMARK 500 O HOH A 560 O HOH A 669 2.19 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 ASP A 314 CB - CG - OD2 ANGL. DEV. = 6.2 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 CYS A 12 -162.30 -165.82 REMARK 500 PHE A 83 -71.98 -133.00 REMARK 500 VAL A 173 -83.67 -96.39 REMARK 500 SER A 197 -51.40 68.69 REMARK 500 ASP A 266 -108.74 45.25 REMARK 500 CYS B 12 -163.97 -165.06 REMARK 500 PHE B 83 -72.66 -135.16 REMARK 500 VAL B 173 -80.03 -97.54 REMARK 500 SER B 197 -53.89 71.58 REMARK 500 ARG B 265 44.87 -143.32 REMARK 500 ASP B 266 -117.12 52.62 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 NA A 347 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AP5 A 346 O1E REMARK 620 2 AP5 A 346 O2D 78.2 REMARK 620 3 HOH A 384 O 117.6 84.9 REMARK 620 4 HOH A 472 O 97.0 161.9 81.9 REMARK 620 5 HOH A 638 O 84.1 95.8 157.8 101.2 REMARK 620 6 HOH A 639 O 149.0 88.6 88.6 103.4 69.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 347 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AP5 B 346 O1E REMARK 620 2 AP5 B 346 O2D 77.4 REMARK 620 3 HOH B 417 O 113.9 79.5 REMARK 620 4 HOH B 630 O 96.1 158.6 84.8 REMARK 620 5 HOH B 631 O 90.6 101.3 154.7 99.1 REMARK 620 6 HOH B 632 O 154.5 92.1 86.2 101.3 68.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AP5 A 346 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 347 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AP5 B 346 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 347 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XTB RELATED DB: PDB DBREF 3OTX A 1 345 UNP Q584S0 Q584S0_9TRYP 1 345 DBREF 3OTX B 1 345 UNP Q584S0 Q584S0_9TRYP 1 345 SEQADV 3OTX GLY A -1 UNP Q584S0 EXPRESSION TAG SEQADV 3OTX SER A 0 UNP Q584S0 EXPRESSION TAG SEQADV 3OTX ALA A 2 UNP Q584S0 SER 2 ENGINEERED MUTATION SEQADV 3OTX GLY B -1 UNP Q584S0 EXPRESSION TAG SEQADV 3OTX SER B 0 UNP Q584S0 EXPRESSION TAG SEQADV 3OTX ALA B 2 UNP Q584S0 SER 2 ENGINEERED MUTATION SEQRES 1 A 347 GLY SER MET ALA SER ALA PRO LEU ARG VAL TYR VAL GLN SEQRES 2 A 347 CYS ASN PRO LEU LEU ASP VAL SER ALA HIS VAL SER ASP SEQRES 3 A 347 GLU PHE LEU VAL LYS TYR GLY LEU GLU ARG GLY THR ALA SEQRES 4 A 347 ILE LEU LEU SER GLU ARG GLN LYS GLY ILE PHE ASP ASP SEQRES 5 A 347 ILE GLU LYS MET PRO ASN VAL ARG TYR VAL PRO GLY GLY SEQRES 6 A 347 SER GLY LEU ASN VAL ALA ARG VAL ALA GLN TRP MET GLN SEQRES 7 A 347 GLN ALA TYR LYS GLY LYS PHE VAL THR TYR VAL GLY CYS SEQRES 8 A 347 ILE ALA ASP ASP ARG TYR GLY LYS VAL LEU LYS GLU ALA SEQRES 9 A 347 ALA GLU HIS GLU GLY ILE VAL MET ALA VAL GLU HIS THR SEQRES 10 A 347 THR LYS ALA GLY SER GLY ALA CYS ALA VAL CYS ILE THR SEQRES 11 A 347 GLY LYS GLU ARG THR LEU VAL ALA ASP LEU GLY ALA ALA SEQRES 12 A 347 ASN HIS LEU SER SER GLU HIS MET ARG SER PRO ALA VAL SEQRES 13 A 347 VAL ARG ALA MET ASP GLU SER ARG ILE PHE TYR PHE SER SEQRES 14 A 347 GLY PHE THR LEU THR VAL ASP VAL ASN HIS VAL LEU GLN SEQRES 15 A 347 ALA CYS ARG LYS ALA ARG GLU VAL ASP GLY LEU PHE MET SEQRES 16 A 347 ILE ASN LEU SER ALA PRO PHE ILE MET GLN PHE PHE SER SEQRES 17 A 347 ALA GLN LEU GLY GLU VAL LEU PRO TYR THR ASP ILE ILE SEQRES 18 A 347 VAL ALA ASN ARG HIS GLU ALA LYS GLU PHE ALA ASN MET SEQRES 19 A 347 MET LYS TRP ASP THR ASP CYS VAL GLU GLU ILE ALA ARG SEQRES 20 A 347 ARG ALA VAL SER GLU VAL PRO TYR THR GLY THR LYS GLY SEQRES 21 A 347 ARG VAL VAL VAL PHE THR ARG ASP ILE GLU SER THR VAL SEQRES 22 A 347 LEU ALA THR LYS ASP GLY VAL GLU THR VAL PRO VAL PRO SEQRES 23 A 347 GLN LEU ASP GLN ASP LYS VAL ILE ASP MET ASN GLY ALA SEQRES 24 A 347 GLY ASP ALA PHE MET GLY GLY PHE LEU SER ALA TYR ALA SEQRES 25 A 347 VAL GLY LYS ASP LEU ARG ARG CYS CYS GLU THR GLY HIS SEQRES 26 A 347 TYR THR ALA GLN GLU VAL ILE GLN ARG ASP GLY CYS SER SEQRES 27 A 347 PHE PRO GLU LYS PRO SER PHE SER PRO SEQRES 1 B 347 GLY SER MET ALA SER ALA PRO LEU ARG VAL TYR VAL GLN SEQRES 2 B 347 CYS ASN PRO LEU LEU ASP VAL SER ALA HIS VAL SER ASP SEQRES 3 B 347 GLU PHE LEU VAL LYS TYR GLY LEU GLU ARG GLY THR ALA SEQRES 4 B 347 ILE LEU LEU SER GLU ARG GLN LYS GLY ILE PHE ASP ASP SEQRES 5 B 347 ILE GLU LYS MET PRO ASN VAL ARG TYR VAL PRO GLY GLY SEQRES 6 B 347 SER GLY LEU ASN VAL ALA ARG VAL ALA GLN TRP MET GLN SEQRES 7 B 347 GLN ALA TYR LYS GLY LYS PHE VAL THR TYR VAL GLY CYS SEQRES 8 B 347 ILE ALA ASP ASP ARG TYR GLY LYS VAL LEU LYS GLU ALA SEQRES 9 B 347 ALA GLU HIS GLU GLY ILE VAL MET ALA VAL GLU HIS THR SEQRES 10 B 347 THR LYS ALA GLY SER GLY ALA CYS ALA VAL CYS ILE THR SEQRES 11 B 347 GLY LYS GLU ARG THR LEU VAL ALA ASP LEU GLY ALA ALA SEQRES 12 B 347 ASN HIS LEU SER SER GLU HIS MET ARG SER PRO ALA VAL SEQRES 13 B 347 VAL ARG ALA MET ASP GLU SER ARG ILE PHE TYR PHE SER SEQRES 14 B 347 GLY PHE THR LEU THR VAL ASP VAL ASN HIS VAL LEU GLN SEQRES 15 B 347 ALA CYS ARG LYS ALA ARG GLU VAL ASP GLY LEU PHE MET SEQRES 16 B 347 ILE ASN LEU SER ALA PRO PHE ILE MET GLN PHE PHE SER SEQRES 17 B 347 ALA GLN LEU GLY GLU VAL LEU PRO TYR THR ASP ILE ILE SEQRES 18 B 347 VAL ALA ASN ARG HIS GLU ALA LYS GLU PHE ALA ASN MET SEQRES 19 B 347 MET LYS TRP ASP THR ASP CYS VAL GLU GLU ILE ALA ARG SEQRES 20 B 347 ARG ALA VAL SER GLU VAL PRO TYR THR GLY THR LYS GLY SEQRES 21 B 347 ARG VAL VAL VAL PHE THR ARG ASP ILE GLU SER THR VAL SEQRES 22 B 347 LEU ALA THR LYS ASP GLY VAL GLU THR VAL PRO VAL PRO SEQRES 23 B 347 GLN LEU ASP GLN ASP LYS VAL ILE ASP MET ASN GLY ALA SEQRES 24 B 347 GLY ASP ALA PHE MET GLY GLY PHE LEU SER ALA TYR ALA SEQRES 25 B 347 VAL GLY LYS ASP LEU ARG ARG CYS CYS GLU THR GLY HIS SEQRES 26 B 347 TYR THR ALA GLN GLU VAL ILE GLN ARG ASP GLY CYS SER SEQRES 27 B 347 PHE PRO GLU LYS PRO SER PHE SER PRO HET AP5 A 346 57 HET NA A 347 1 HET AP5 B 346 57 HET NA B 347 1 HETNAM AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE HETNAM NA SODIUM ION FORMUL 3 AP5 2(C20 H29 N10 O22 P5) FORMUL 4 NA 2(NA 1+) FORMUL 7 HOH *626(H2 O) HELIX 1 1 SER A 23 TYR A 30 1 8 HELIX 2 2 SER A 41 LYS A 45 5 5 HELIX 3 3 GLY A 46 LYS A 53 1 8 HELIX 4 4 GLY A 63 MET A 75 1 13 HELIX 5 5 GLN A 76 LYS A 80 5 5 HELIX 6 6 ASP A 93 GLY A 107 1 15 HELIX 7 7 ALA A 141 LEU A 144 5 4 HELIX 8 8 SER A 145 ARG A 150 1 6 HELIX 9 9 SER A 151 SER A 161 1 11 HELIX 10 10 PHE A 169 VAL A 173 5 5 HELIX 11 11 ASP A 174 VAL A 188 1 15 HELIX 12 12 ALA A 198 PHE A 205 1 8 HELIX 13 13 PHE A 205 LEU A 213 1 9 HELIX 14 14 PRO A 214 THR A 216 5 3 HELIX 15 15 ARG A 223 LYS A 234 1 12 HELIX 16 16 CYS A 239 GLU A 250 1 12 HELIX 17 17 ASP A 287 VAL A 291 5 5 HELIX 18 18 ALA A 297 ALA A 310 1 14 HELIX 19 19 ASP A 314 GLN A 331 1 18 HELIX 20 20 SER B 23 TYR B 30 1 8 HELIX 21 21 SER B 41 LYS B 45 5 5 HELIX 22 22 GLY B 46 GLU B 52 1 7 HELIX 23 23 GLY B 63 MET B 75 1 13 HELIX 24 24 GLN B 76 LYS B 80 5 5 HELIX 25 25 ASP B 93 GLY B 107 1 15 HELIX 26 26 ALA B 141 LEU B 144 5 4 HELIX 27 27 SER B 145 ARG B 150 1 6 HELIX 28 28 SER B 151 SER B 161 1 11 HELIX 29 29 PHE B 169 VAL B 173 5 5 HELIX 30 30 ASP B 174 VAL B 188 1 15 HELIX 31 31 ALA B 198 PHE B 205 1 8 HELIX 32 32 PHE B 205 LEU B 213 1 9 HELIX 33 33 PRO B 214 THR B 216 5 3 HELIX 34 34 ARG B 223 MET B 233 1 11 HELIX 35 35 CYS B 239 GLU B 250 1 12 HELIX 36 36 ASP B 287 VAL B 291 5 5 HELIX 37 37 ALA B 297 ALA B 310 1 14 HELIX 38 38 ASP B 314 GLN B 331 1 18 SHEET 1 A 9 VAL A 109 MET A 110 0 SHEET 2 A 9 VAL A 84 VAL A 87 1 N TYR A 86 O VAL A 109 SHEET 3 A 9 VAL A 8 GLN A 11 1 N VAL A 10 O THR A 85 SHEET 4 A 9 ILE A 163 SER A 167 1 O TYR A 165 N TYR A 9 SHEET 5 A 9 LEU A 191 ASN A 195 1 O MET A 193 N PHE A 164 SHEET 6 A 9 ILE A 218 ASN A 222 1 O VAL A 220 N ILE A 194 SHEET 7 A 9 VAL A 260 ARG A 265 1 O VAL A 262 N ILE A 219 SHEET 8 A 9 GLU A 268 THR A 274 -1 O VAL A 271 N PHE A 263 SHEET 9 A 9 GLY A 277 VAL A 281 -1 O GLU A 279 N LEU A 272 SHEET 1 B 5 ALA A 37 LEU A 39 0 SHEET 2 B 5 GLU A 131 GLY A 139 1 O ALA A 136 N ILE A 38 SHEET 3 B 5 SER A 120 THR A 128 -1 N ALA A 122 O ASP A 137 SHEET 4 B 5 LEU A 15 HIS A 21 1 N VAL A 18 O VAL A 125 SHEET 5 B 5 ARG A 58 PRO A 61 -1 O VAL A 60 N ASP A 17 SHEET 1 C 2 CYS A 89 ILE A 90 0 SHEET 2 C 2 GLU A 113 HIS A 114 1 O GLU A 113 N ILE A 90 SHEET 1 D 9 VAL B 109 MET B 110 0 SHEET 2 D 9 VAL B 84 VAL B 87 1 N TYR B 86 O VAL B 109 SHEET 3 D 9 VAL B 8 GLN B 11 1 N VAL B 10 O THR B 85 SHEET 4 D 9 ILE B 163 SER B 167 1 O ILE B 163 N TYR B 9 SHEET 5 D 9 LEU B 191 ASN B 195 1 O MET B 193 N PHE B 164 SHEET 6 D 9 ILE B 218 ASN B 222 1 O ILE B 218 N ILE B 194 SHEET 7 D 9 VAL B 260 ARG B 265 1 O VAL B 262 N ILE B 219 SHEET 8 D 9 GLU B 268 THR B 274 -1 O VAL B 271 N PHE B 263 SHEET 9 D 9 GLY B 277 VAL B 281 -1 O GLU B 279 N LEU B 272 SHEET 1 E 5 ALA B 37 LEU B 39 0 SHEET 2 E 5 GLU B 131 GLY B 139 1 O ALA B 136 N ILE B 38 SHEET 3 E 5 SER B 120 THR B 128 -1 N ALA B 122 O ASP B 137 SHEET 4 E 5 LEU B 15 HIS B 21 1 N ALA B 20 O ILE B 127 SHEET 5 E 5 ARG B 58 PRO B 61 -1 O VAL B 60 N ASP B 17 SHEET 1 F 2 CYS B 89 ALA B 91 0 SHEET 2 F 2 GLU B 113 THR B 115 1 O GLU B 113 N ILE B 90 SSBOND 1 CYS A 239 CYS B 335 1555 1555 2.04 LINK O1E AP5 A 346 NA NA A 347 1555 1555 2.37 LINK O2D AP5 A 346 NA NA A 347 1555 1555 2.59 LINK NA NA A 347 O HOH A 384 1555 1555 2.54 LINK NA NA A 347 O HOH A 472 1555 1555 2.40 LINK NA NA A 347 O HOH A 638 1555 1555 2.59 LINK NA NA A 347 O HOH A 639 1555 1555 2.28 LINK O1E AP5 B 346 NA NA B 347 1555 1555 2.47 LINK O2D AP5 B 346 NA NA B 347 1555 1555 2.70 LINK NA NA B 347 O HOH B 417 1555 1555 2.38 LINK NA NA B 347 O HOH B 630 1555 1555 2.40 LINK NA NA B 347 O HOH B 631 1555 1555 2.37 LINK NA NA B 347 O HOH B 632 1555 1555 2.26 SITE 1 AC1 50 CYS A 12 ASN A 13 LEU A 15 ASP A 17 SITE 2 AC1 50 LEU A 39 GLY A 62 GLY A 63 SER A 64 SITE 3 AC1 50 ASN A 67 CYS A 123 ARG A 132 ALA A 136 SITE 4 AC1 50 PHE A 169 ASN A 222 THR A 264 ARG A 265 SITE 5 AC1 50 ASP A 266 ILE A 267 THR A 270 VAL A 283 SITE 6 AC1 50 GLN A 288 GLY A 296 ALA A 297 GLY A 298 SITE 7 AC1 50 ASP A 299 HIS A 323 ALA A 326 GLN A 327 SITE 8 AC1 50 ILE A 330 NA A 347 HOH A 355 HOH A 357 SITE 9 AC1 50 HOH A 364 HOH A 368 HOH A 384 HOH A 448 SITE 10 AC1 50 HOH A 449 HOH A 452 HOH A 456 HOH A 459 SITE 11 AC1 50 HOH A 464 HOH A 506 HOH A 515 HOH A 518 SITE 12 AC1 50 HOH A 564 HOH A 585 HOH A 637 HOH A 638 SITE 13 AC1 50 HOH A 642 HOH A 685 SITE 1 AC2 6 ASP A 299 AP5 A 346 HOH A 384 HOH A 472 SITE 2 AC2 6 HOH A 638 HOH A 639 SITE 1 AC3 49 HIS A 105 CYS B 12 ASN B 13 LEU B 15 SITE 2 AC3 49 ASP B 17 LEU B 39 GLY B 62 GLY B 63 SITE 3 AC3 49 SER B 64 ASN B 67 ARG B 132 ALA B 136 SITE 4 AC3 49 LEU B 138 PHE B 169 ASN B 222 THR B 264 SITE 5 AC3 49 ARG B 265 ASP B 266 ILE B 267 THR B 270 SITE 6 AC3 49 VAL B 283 GLN B 288 GLY B 296 ALA B 297 SITE 7 AC3 49 GLY B 298 ASP B 299 HIS B 323 ALA B 326 SITE 8 AC3 49 GLN B 327 ILE B 330 NA B 347 HOH B 367 SITE 9 AC3 49 HOH B 385 HOH B 389 HOH B 396 HOH B 400 SITE 10 AC3 49 HOH B 404 HOH B 409 HOH B 417 HOH B 419 SITE 11 AC3 49 HOH B 420 HOH B 424 HOH B 426 HOH B 437 SITE 12 AC3 49 HOH B 448 HOH B 555 HOH B 581 HOH B 583 SITE 13 AC3 49 HOH B 631 SITE 1 AC4 6 ASP B 299 AP5 B 346 HOH B 417 HOH B 630 SITE 2 AC4 6 HOH B 631 HOH B 632 CRYST1 68.893 70.549 72.410 90.00 90.77 90.00 P 1 21 1 4 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 0.014515 0.000000 0.000195 0.00000 SCALE2 0.000000 0.014175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013811 0.00000