HEADER HYDROLASE, LIGASE 05-JUN-09 3A2Z TITLE E. COLI GSP AMIDASE CYS59 SULFENIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL GLUTATHIONYLSPERMIDINE SYNTHETASE/AMIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-197; COMPND 5 SYNONYM: GLUTATHIONYLSPERMIDINE SYNTHASE, GLUTATHIONE:SPERMIDINE COMPND 6 LIGASE [ADP-FORMING], GSP SYNTHETASE, GLUTATHIONYLSPERMIDINE AMIDASE, COMPND 7 GLUTATHIONYLSPERMIDINE AMIDOHYDROLASE [SPERMIDINE-FORMING], GSP COMPND 8 AMIDASE; COMPND 9 EC: 6.3.1.8, 3.5.1.78; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: GSP, B2988, JW2956; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS GSP AMIDASE, ATP-BINDING, HYDROLASE, LIGASE, MULTIFUNCTIONAL ENZYME, KEYWDS 2 NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR C.-H.PAI,T.-P.KO,B.-Y.CHIANG,C.-H.LIN,A.H.-J.WANG REVDAT 5 01-NOV-23 3A2Z 1 REMARK REVDAT 4 10-MAR-21 3A2Z 1 REMARK LINK REVDAT 3 11-OCT-17 3A2Z 1 REMARK REVDAT 2 17-NOV-10 3A2Z 1 JRNL REVDAT 1 19-MAY-10 3A2Z 0 JRNL AUTH B.-Y.CHIANG,T.-C.CHEN,C.-H.PAI,C.-C.CHOU,H.-H.CHEN,T.-P.KO, JRNL AUTH 2 W.-H.HSU,C.-Y.CHANG,W.-F.WU,A.H.-J.WANG,C.-H.LIN JRNL TITL PROTEIN S-THIOLATION BY GLUTATHIONYLSPERMIDINE (GSP): THE JRNL TITL 2 ROLE OF ESCHERICHIA COLI GSP SYNTHETASE/AMIDASE IN REDOX JRNL TITL 3 REGULATION JRNL REF J.BIOL.CHEM. V. 285 25345 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20530482 JRNL DOI 10.1074/JBC.M110.133363 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 34651 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 SET) : 0.180 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1719 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2239 REMARK 3 BIN FREE R VALUE : 0.2742 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 164 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1526 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 364 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.07900 REMARK 3 B22 (A**2) : -1.07900 REMARK 3 B33 (A**2) : 2.15800 REMARK 3 B12 (A**2) : -0.92000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.11 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 1.866 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.493 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.397 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.233 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.280 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 48.92 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : PROSTH.PAR REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3A2Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000028746. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35956 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 17.00 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 77.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 15.10 REMARK 200 R MERGE FOR SHELL (I) : 0.59700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2IOB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M ACETATE, 0.8M NAH2PO4, 1.2M REMARK 280 K2HPO4, PH 4.5, EVAPORATION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.51033 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 71.02067 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.51033 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 71.02067 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 35.51033 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 71.02067 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 35.51033 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 71.02067 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 501 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 534 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 670 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 792 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 814 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 855 LIES ON A SPECIAL POSITION. 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 SER A 2 REMARK 465 LYS A 3 REMARK 465 GLY A 4 REMARK 465 THR A 5 REMARK 465 THR A 6 REMARK 465 SER A 7 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 537 O HOH A 632 1.88 REMARK 500 N HIS A 152 O HOH A 802 1.92 REMARK 500 O HOH A 558 O HOH A 766 2.01 REMARK 500 O HOH A 632 O HOH A 836 2.01 REMARK 500 O HOH A 560 O HOH A 794 2.07 REMARK 500 O HOH A 596 O HOH A 853 2.08 REMARK 500 O HOH A 632 O HOH A 835 2.09 REMARK 500 O HOH A 599 O HOH A 781 2.10 REMARK 500 O HOH A 633 O HOH A 835 2.10 REMARK 500 SG CYS A 59 O HOH A 900 2.14 REMARK 500 O HOH A 671 O HOH A 845 2.14 REMARK 500 O HOH A 631 O HOH A 836 2.16 REMARK 500 O HOH A 754 O HOH A 843 2.18 REMARK 500 O HOH A 675 O HOH A 733 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 813 O HOH A 813 11655 2.03 REMARK 500 O HOH A 782 O HOH A 782 11555 2.09 REMARK 500 O HOH A 771 O HOH A 771 8555 2.15 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 110 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 110 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP A 121 CB - CG - OD2 ANGL. DEV. = -5.9 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 ASP A 50 -5.32 68.58 REMARK 500 ASP A 77 79.02 -66.82 REMARK 500 LYS A 127 -119.24 33.43 REMARK 500 VAL A 150 -59.18 -123.77 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 A 674 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A 728 DISTANCE = 10.27 ANGSTROMS REMARK 525 HOH A 740 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A 742 DISTANCE = 8.15 ANGSTROMS REMARK 525 HOH A 743 DISTANCE = 11.20 ANGSTROMS REMARK 525 HOH A 744 DISTANCE = 7.93 ANGSTROMS REMARK 525 HOH A 749 DISTANCE = 12.54 ANGSTROMS REMARK 525 HOH A 750 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A 751 DISTANCE = 8.39 ANGSTROMS REMARK 525 HOH A 772 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A 776 DISTANCE = 9.06 ANGSTROMS REMARK 525 HOH A 777 DISTANCE = 8.89 ANGSTROMS REMARK 525 HOH A 782 DISTANCE = 10.26 ANGSTROMS REMARK 525 HOH A 783 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A 789 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A 799 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A 803 DISTANCE = 7.54 ANGSTROMS REMARK 525 HOH A 807 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH A 814 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH A 816 DISTANCE = 7.15 ANGSTROMS REMARK 525 HOH A 817 DISTANCE = 10.26 ANGSTROMS REMARK 525 HOH A 818 DISTANCE = 9.28 ANGSTROMS REMARK 525 HOH A 819 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A 820 DISTANCE = 7.16 ANGSTROMS REMARK 525 HOH A 822 DISTANCE = 9.71 ANGSTROMS REMARK 525 HOH A 825 DISTANCE = 10.28 ANGSTROMS REMARK 525 HOH A 830 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A 831 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A 833 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A 849 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A 851 DISTANCE = 7.42 ANGSTROMS REMARK 525 HOH A 857 DISTANCE = 9.13 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 ACCORDING TO THE DEPOSITOR, THEY OBSERVED THE MODIFICATION ON CYS59 REMARK 600 WITH EXTENDED DENSITY MAP, AND INTERPRET THIS CYS59 AS CYS-S-O, THE REMARK 600 SULFENIC ACID IN THIS ENTRY. HYDROGEN PEROXIDE CONSIST OF HOH A 900 REMARK 600 AND 901 DONATED OXYGEN OF CYS-S-O. SINCE IT WAS KIND OF LIKE AN REMARK 600 INTERMEDIATE, THE DISTANCE OF S-O IS LARGER THAN IT USUALLY IS. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IOB RELATED DB: PDB REMARK 900 MODEL FOR MOLECULAR REPLACEMENT REMARK 900 RELATED ID: 3A2Y RELATED DB: PDB REMARK 900 E. COLI GSP AMIDASE C59A COMPLEXED WITH GSP REMARK 900 RELATED ID: 3A30 RELATED DB: PDB REMARK 900 E. COLI GSP AMIDASE CYS59 ACETATE MODIFICATION DBREF 3A2Z A 1 197 UNP P0AES0 GSP_ECOLI 1 197 SEQRES 1 A 197 MET SER LYS GLY THR THR SER GLN ASP ALA PRO PHE GLY SEQRES 2 A 197 THR LEU LEU GLY TYR ALA PRO GLY GLY VAL ALA ILE TYR SEQRES 3 A 197 SER SER ASP TYR SER SER LEU ASP PRO GLN GLU TYR GLU SEQRES 4 A 197 ASP ASP ALA VAL PHE ARG SER TYR ILE ASP ASP GLU TYR SEQRES 5 A 197 MET GLY HIS LYS TRP GLN CYS VAL GLU PHE ALA ARG ARG SEQRES 6 A 197 PHE LEU PHE LEU ASN TYR GLY VAL VAL PHE THR ASP VAL SEQRES 7 A 197 GLY MET ALA TRP GLU ILE PHE SER LEU ARG PHE LEU ARG SEQRES 8 A 197 GLU VAL VAL ASN ASP ASN ILE LEU PRO LEU GLN ALA PHE SEQRES 9 A 197 PRO ASN GLY SER PRO ARG ALA PRO VAL ALA GLY ALA LEU SEQRES 10 A 197 LEU ILE TRP ASP LYS GLY GLY GLU PHE LYS ASP THR GLY SEQRES 11 A 197 HIS VAL ALA ILE ILE THR GLN LEU HIS GLY ASN LYS VAL SEQRES 12 A 197 ARG ILE ALA GLU GLN ASN VAL ILE HIS SER PRO LEU PRO SEQRES 13 A 197 GLN GLY GLN GLN TRP THR ARG GLU LEU GLU MET VAL VAL SEQRES 14 A 197 GLU ASN GLY CYS TYR THR LEU LYS ASP THR PHE ASP ASP SEQRES 15 A 197 THR THR ILE LEU GLY TRP MET ILE GLN THR GLU ASP THR SEQRES 16 A 197 GLU TYR FORMUL 2 HOH *364(H2 O) HELIX 1 1 ASP A 34 ASP A 41 1 8 HELIX 2 2 GLN A 58 GLY A 72 1 15 HELIX 3 3 MET A 80 LEU A 87 5 8 HELIX 4 4 GLY A 123 LYS A 127 5 5 SHEET 1 A 2 LEU A 15 ALA A 19 0 SHEET 2 A 2 VAL A 23 TYR A 26 -1 O ILE A 25 N LEU A 16 SHEET 1 B 2 ARG A 45 ILE A 48 0 SHEET 2 B 2 GLU A 51 HIS A 55 -1 O MET A 53 N SER A 46 SHEET 1 C 3 VAL A 73 VAL A 74 0 SHEET 2 C 3 PHE A 89 GLU A 92 -1 O ARG A 91 N VAL A 74 SHEET 3 C 3 ILE A 98 PRO A 100 -1 O LEU A 99 N LEU A 90 SHEET 1 D 7 GLN A 102 PRO A 105 0 SHEET 2 D 7 ILE A 185 ILE A 190 -1 O TRP A 188 N PHE A 104 SHEET 3 D 7 LEU A 117 TRP A 120 -1 N ILE A 119 O GLY A 187 SHEET 4 D 7 HIS A 131 LEU A 138 -1 O ALA A 133 N LEU A 118 SHEET 5 D 7 LYS A 142 ALA A 146 -1 O ARG A 144 N THR A 136 SHEET 6 D 7 ARG A 163 GLU A 170 -1 O ARG A 163 N ILE A 145 SHEET 7 D 7 CYS A 173 LYS A 177 -1 O THR A 175 N VAL A 168 CISPEP 1 LYS A 56 TRP A 57 0 -10.61 CRYST1 83.902 83.902 106.531 90.00 90.00 120.00 P 64 2 2 12 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 0.011919 0.006881 0.000000 0.00000 SCALE2 0.000000 0.013762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009387 0.00000