HEADER HYDROLASE 02-MAR-15 5AK8 TITLE STRUCTURE OF C351A MUTANT OF PORPHYROMONAS GINGIVALIS PEPTIDYLARGININE TITLE 2 DEIMINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYLARGININE DEIMINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 49-484; COMPND 5 SYNONYM: PPAD; COMPND 6 EC: 3.5.3.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYROMONAS GINGIVALIS; SOURCE 3 ORGANISM_TAXID: 837; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA KEYWDS HYDROLASE, PPAD EXPDTA X-RAY DIFFRACTION AUTHOR J.KOPEC,A.MONTGOMERY,L.SHRESTHA,W.KIYANI,R.NOWAK,N.BURGESS-BROWN, AUTHOR 2 P.J.VENABLES,W.W.YUE REVDAT 5 20-JUN-18 5AK8 1 REMARK LINK REVDAT 4 25-MAY-16 5AK8 1 JRNL REVDAT 3 19-AUG-15 5AK8 1 COMPND KEYWDS REVDAT 2 05-AUG-15 5AK8 1 JRNL REVDAT 1 22-JUL-15 5AK8 0 JRNL AUTH A.B.MONTGOMERY,J.KOPEC,L.SHRESTHA,M.L.THEZENAS, JRNL AUTH 2 N.A.BURGESS-BROWN,R.FISCHER,W.W.YUE,P.J.VENABLES JRNL TITL CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS JRNL TITL 2 PEPTIDYLARGININE DEIMINASE: IMPLICATIONS FOR AUTOIMMUNITY IN JRNL TITL 3 RHEUMATOID ARTHRITIS. JRNL REF ANN.RHEUM.DIS. V. 75 1255 2016 JRNL REFN ISSN 0003-4967 JRNL PMID 26209657 JRNL DOI 10.1136/ANNRHEUMDIS-2015-207656 REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 70193 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) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.127 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3636 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) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5083 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 242 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3288 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 462 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.69000 REMARK 3 B22 (A**2) : -0.44000 REMARK 3 B33 (A**2) : -0.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.44000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.064 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.059 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.064 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3480 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3196 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4705 ; 1.580 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7354 ; 0.987 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 431 ; 6.077 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 166 ;34.442 ;24.819 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 533 ;11.007 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;11.153 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 499 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3971 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 810 ; 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): 1697 ; 2.643 ; 1.766 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1696 ; 2.644 ; 1.766 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2122 ; 3.312 ; 2.663 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1783 ; 3.206 ; 1.948 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): 6676 ; 2.476 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 156 ;41.368 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6909 ;17.768 ; 5.000 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 5AK8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1290063178. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73831 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 64.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 30% PEG5000MME, REMARK 280 0.1M MES PH 6.5 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 50.89500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.04500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.89500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 42.04500 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: 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 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 THR A 466 REMARK 465 ASN A 467 REMARK 465 THR A 468 REMARK 465 CYS A 469 REMARK 465 THR A 470 REMARK 465 VAL A 471 REMARK 465 THR A 472 REMARK 465 GLY A 473 REMARK 465 ALA A 474 REMARK 465 ALA A 475 REMARK 465 LYS A 476 REMARK 465 ALA A 477 REMARK 465 LEU A 478 REMARK 465 ARG A 479 REMARK 465 ALA A 480 REMARK 465 TRP A 481 REMARK 465 PHE A 482 REMARK 465 ASN A 483 REMARK 465 ALA A 484 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 LYS A 85 CD CE NZ REMARK 470 LYS A 122 CD CE NZ REMARK 470 LYS A 408 CD CE NZ REMARK 470 LYS A 429 CD CE NZ REMARK 470 LYS A 446 CE NZ 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 C ALA A 1001 N ARG A 1002 1.34 REMARK 500 O HOH A 2159 O HOH A 2321 2.10 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 ASN A 112 94.96 -68.55 REMARK 500 THR A 140 -51.73 71.54 REMARK 500 ASN A 151 34.99 -79.39 REMARK 500 TRP A 240 -18.46 -141.17 REMARK 500 ASN A 291 44.96 -140.35 REMARK 500 ASN A 302 -119.39 54.06 REMARK 500 ASN A 310 28.77 -150.11 REMARK 500 ASP A 347 100.37 -167.49 REMARK 500 ALA A 348 -137.33 -138.70 REMARK 500 SER A 393 135.59 -176.02 REMARK 500 ASN A 430 -2.14 79.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 ALA A 1001 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 A1466 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 147 OD1 REMARK 620 2 PHE A 148 O 83.0 REMARK 620 3 ASP A 158 O 104.9 161.9 REMARK 620 4 ASP A 158 OD1 161.9 86.3 81.7 REMARK 620 5 HOH A2134 O 80.9 95.8 70.0 85.7 REMARK 620 6 HOH A2114 O 96.8 94.1 101.0 98.4 169.6 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 NA A 1466 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1467 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1468 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1469 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1470 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1471 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1472 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1473 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1474 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1475 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1476 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1477 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1478 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1479 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1480 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1481 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1482 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1483 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1484 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: Binding site for Di-peptide ALA A1001 and ARG REMARK 800 A1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AK7 RELATED DB: PDB REMARK 900 STRUCTURE OF WT PORPHYROMONAS GINGIVALIS PEPTIDYLARGININE DEIMINASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 C351A - CATALYTIC MUTANT DBREF 5AK8 A 49 484 UNP Q9RQJ2 PAD_PORGI 49 484 SEQADV 5AK8 SER A 47 UNP Q9RQJ2 EXPRESSION TAG SEQADV 5AK8 MET A 48 UNP Q9RQJ2 EXPRESSION TAG SEQADV 5AK8 ALA A 351 UNP Q9RQJ2 CYS 351 ENGINEERED MUTATION SEQRES 1 A 438 SER MET ASN PRO PRO ALA GLY PRO VAL ARG ALA ILE ALA SEQRES 2 A 438 GLU TYR GLU ARG SER ALA ALA VAL LEU VAL ARG TYR PRO SEQRES 3 A 438 PHE GLY ILE PRO MET GLU LEU ILE LYS GLU LEU ALA LYS SEQRES 4 A 438 ASN ASP LYS VAL ILE THR ILE VAL ALA SER GLU SER GLN SEQRES 5 A 438 LYS ASN THR VAL ILE THR GLN TYR THR GLN SER GLY VAL SEQRES 6 A 438 ASN LEU SER ASN CYS ASP PHE ILE ILE ALA LYS THR ASP SEQRES 7 A 438 SER TYR TRP THR ARG ASP TYR THR GLY TRP PHE ALA MET SEQRES 8 A 438 TYR ASP THR ASN LYS VAL GLY LEU VAL ASP PHE ILE TYR SEQRES 9 A 438 ASN ARG PRO ARG PRO ASN ASP ASP GLU PHE PRO LYS TYR SEQRES 10 A 438 GLU ALA GLN TYR LEU GLY ILE GLU MET PHE GLY MET LYS SEQRES 11 A 438 LEU LYS GLN THR GLY GLY ASN TYR MET THR ASP GLY TYR SEQRES 12 A 438 GLY SER ALA VAL GLN SER HIS ILE ALA TYR THR GLU ASN SEQRES 13 A 438 SER SER LEU SER GLN ALA GLN VAL ASN GLN LYS MET LYS SEQRES 14 A 438 ASP TYR LEU GLY ILE THR HIS HIS ASP VAL VAL GLN ASP SEQRES 15 A 438 PRO ASN GLY GLU TYR ILE ASN HIS VAL ASP CYS TRP GLY SEQRES 16 A 438 LYS TYR LEU ALA PRO ASN LYS ILE LEU ILE ARG LYS VAL SEQRES 17 A 438 PRO ASP ASN HIS PRO GLN HIS GLN ALA LEU GLU ASP MET SEQRES 18 A 438 ALA ALA TYR PHE ALA ALA GLN THR CYS ALA TRP GLY THR SEQRES 19 A 438 LYS TYR GLU VAL TYR ARG ALA LEU ALA THR ASN GLU GLN SEQRES 20 A 438 PRO TYR THR ASN SER LEU ILE LEU ASN ASN ARG VAL PHE SEQRES 21 A 438 VAL PRO VAL ASN GLY PRO ALA SER VAL ASP ASN ASP ALA SEQRES 22 A 438 LEU ASN VAL TYR LYS THR ALA MET PRO GLY TYR GLU ILE SEQRES 23 A 438 ILE GLY VAL LYS GLY ALA SER GLY THR PRO TRP LEU GLY SEQRES 24 A 438 THR ASP ALA LEU HIS ALA ARG THR HIS GLU VAL ALA ASP SEQRES 25 A 438 LYS GLY TYR LEU TYR ILE LYS HIS TYR PRO ILE LEU GLY SEQRES 26 A 438 GLU GLN ALA GLY PRO ASP TYR LYS ILE GLU ALA ASP VAL SEQRES 27 A 438 VAL SER CYS ALA ASN ALA THR ILE SER PRO VAL GLN CYS SEQRES 28 A 438 TYR TYR ARG ILE ASN GLY SER GLY SER PHE LYS ALA ALA SEQRES 29 A 438 ASP MET THR MET GLU SER THR GLY HIS TYR THR TYR SER SEQRES 30 A 438 PHE THR GLY LEU ASN LYS ASN ASP LYS VAL GLU TYR TYR SEQRES 31 A 438 ILE SER ALA ALA ASP ASN SER GLY ARG LYS GLU THR TYR SEQRES 32 A 438 PRO PHE ILE GLY GLU PRO ASP PRO PHE LYS PHE THR CYS SEQRES 33 A 438 MET ASN GLU THR ASN THR CYS THR VAL THR GLY ALA ALA SEQRES 34 A 438 LYS ALA LEU ARG ALA TRP PHE ASN ALA HET ALA A1001 5 HET ARG A1002 12 HET NA A1466 1 HET EDO A1467 4 HET EDO A1468 4 HET EDO A1469 4 HET EDO A1470 4 HET EDO A1471 4 HET EDO A1472 4 HET EDO A1473 4 HET EDO A1474 4 HET EDO A1475 4 HET EDO A1476 4 HET EDO A1477 4 HET EDO A1478 4 HET EDO A1479 4 HET EDO A1480 4 HET EDO A1481 4 HET EDO A1482 4 HET EDO A1483 4 HET EDO A1484 4 HETNAM ALA ALANINE HETNAM ARG ARGININE HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ALA C3 H7 N O2 FORMUL 3 ARG C6 H15 N4 O2 1+ FORMUL 4 NA NA 1+ FORMUL 5 EDO 18(C2 H6 O2) FORMUL 23 HOH *462(H2 O) HELIX 1 1 PRO A 76 ASP A 87 1 12 HELIX 2 2 SER A 95 SER A 109 1 15 HELIX 3 3 ASN A 112 SER A 114 5 3 HELIX 4 4 TRP A 127 THR A 132 1 6 HELIX 5 5 ARG A 154 PHE A 160 1 7 HELIX 6 6 PHE A 160 GLY A 169 1 10 HELIX 7 7 THR A 180 TYR A 184 5 5 HELIX 8 8 HIS A 196 GLU A 201 1 6 HELIX 9 9 SER A 206 GLY A 219 1 14 HELIX 10 10 HIS A 236 CYS A 239 5 4 HELIX 11 11 GLN A 260 ALA A 273 1 14 HELIX 12 12 PRO A 312 MET A 327 1 16 HELIX 13 13 LEU A 349 THR A 353 5 5 SHEET 1 AA 4 ARG A 56 ALA A 57 0 SHEET 2 AA 4 TRP A 134 TYR A 138 -1 O MET A 137 N ARG A 56 SHEET 3 AA 4 LYS A 142 TYR A 150 -1 O LYS A 142 N TYR A 138 SHEET 4 AA 4 MET A 172 GLN A 179 1 O PHE A 173 N ASP A 147 SHEET 1 AB 4 CYS A 116 ILE A 120 0 SHEET 2 AB 4 VAL A 89 VAL A 93 1 O VAL A 89 N ASP A 117 SHEET 3 AB 4 SER A 64 ARG A 70 1 O VAL A 67 N ILE A 90 SHEET 4 AB 4 HIS A 354 ALA A 357 -1 O HIS A 354 N LEU A 68 SHEET 1 AC 3 MET A 185 THR A 186 0 SHEET 2 AC 3 SER A 191 SER A 195 -1 O VAL A 193 N MET A 185 SHEET 3 AC 3 HIS A 222 VAL A 226 1 O HIS A 222 N ALA A 192 SHEET 1 AD 3 GLY A 241 ALA A 245 0 SHEET 2 AD 3 LYS A 248 LYS A 253 -1 O LYS A 248 N LEU A 244 SHEET 3 AD 3 GLU A 283 LEU A 288 1 O GLU A 283 N ILE A 249 SHEET 1 AE 3 LEU A 299 LEU A 301 0 SHEET 2 AE 3 ARG A 304 VAL A 309 -1 O ARG A 304 N LEU A 301 SHEET 3 AE 3 GLU A 331 LYS A 336 1 O GLU A 331 N VAL A 305 SHEET 1 AF 4 LEU A 362 HIS A 366 0 SHEET 2 AF 4 LYS A 379 SER A 386 -1 O ASP A 383 N LYS A 365 SHEET 3 AF 4 HIS A 419 SER A 423 -1 O TYR A 420 N ALA A 382 SHEET 4 AF 4 THR A 413 SER A 416 -1 O THR A 413 N THR A 421 SHEET 1 AG 4 GLY A 371 GLN A 373 0 SHEET 2 AG 4 PHE A 458 CYS A 462 1 O LYS A 459 N GLY A 371 SHEET 3 AG 4 LYS A 432 ASP A 441 -1 O VAL A 433 N PHE A 460 SHEET 4 AG 4 LYS A 446 TYR A 449 1 O GLU A 447 N ALA A 439 SHEET 1 AH 5 GLY A 371 GLN A 373 0 SHEET 2 AH 5 PHE A 458 CYS A 462 1 O LYS A 459 N GLY A 371 SHEET 3 AH 5 LYS A 432 ASP A 441 -1 O VAL A 433 N PHE A 460 SHEET 4 AH 5 ILE A 392 ILE A 401 -1 N SER A 393 O ALA A 440 SHEET 5 AH 5 LYS A 408 ASP A 411 -1 O LYS A 408 N TYR A 399 SHEET 1 AI 2 LYS A 446 TYR A 449 0 SHEET 2 AI 2 LYS A 432 ASP A 441 1 O ILE A 437 N TYR A 449 LINK OD1 ASP A 147 NA NA A1466 1555 1555 2.35 LINK O PHE A 148 NA NA A1466 1555 1555 2.34 LINK O ASP A 158 NA NA A1466 1555 1555 2.39 LINK OD1 ASP A 158 NA NA A1466 1555 1555 2.33 LINK NA NA A1466 O HOH A2134 1555 1555 2.71 LINK NA NA A1466 O HOH A2114 1555 1555 2.33 CISPEP 1 GLY A 53 PRO A 54 0 -0.01 CISPEP 2 TYR A 71 PRO A 72 0 3.30 CISPEP 3 GLY A 311 PRO A 312 0 -7.70 CISPEP 4 GLY A 375 PRO A 376 0 1.07 CISPEP 5 SER A 393 PRO A 394 0 -7.09 CISPEP 6 TYR A 449 PRO A 450 0 0.86 SITE 1 AC1 5 ASP A 147 PHE A 148 ASP A 158 HOH A2114 SITE 2 AC1 5 HOH A2134 SITE 1 AC2 7 TYR A 61 GLU A 62 PRO A 246 TYR A 361 SITE 2 AC2 7 TYR A 449 HOH A2023 HOH A2363 SITE 1 AC3 4 SER A 125 TYR A 126 TRP A 127 EDO A1472 SITE 1 AC4 8 LYS A 248 GLU A 283 TYR A 285 ALA A 326 SITE 2 AC4 8 PRO A 328 ASP A 456 EDO A1474 HOH A2291 SITE 1 AC5 8 ILE A 58 GLU A 60 ARG A 129 MET A 185 SITE 2 AC5 8 THR A 186 GLU A 355 HOH A2019 HOH A2021 SITE 1 AC6 7 LYS A 365 TYR A 367 GLU A 381 ASP A 383 SITE 2 AC6 7 HIS A 419 HOH A2366 HOH A2455 SITE 1 AC7 4 ARG A 70 TYR A 126 EDO A1468 HOH A2041 SITE 1 AC8 4 LYS A 176 ASN A 202 HOH A2209 HOH A2211 SITE 1 AC9 8 ASN A 247 PRO A 450 ASP A 456 PRO A 457 SITE 2 AC9 8 PHE A 458 EDO A1469 EDO A1483 HOH A2291 SITE 1 BC1 6 PRO A 54 ARG A 56 TYR A 138 THR A 140 SITE 2 BC1 6 TYR A 363 HOH A2457 SITE 1 BC2 3 TYR A 270 HOH A2236 HOH A2273 SITE 1 BC3 5 TYR A 399 TYR A 422 PHE A 424 THR A 425 SITE 2 BC3 5 LEU A 427 SITE 1 BC4 6 ASP A 117 PHE A 118 TYR A 167 LYS A 281 SITE 2 BC4 6 HOH A2283 HOH A2458 SITE 1 BC5 4 ARG A 63 ARG A 445 LYS A 446 GLU A 447 SITE 1 BC6 3 PRO A 455 LYS A 459 HOH A2430 SITE 1 BC7 3 ALA A 409 ALA A 410 ASP A 411 SITE 1 BC8 6 PRO A 54 VAL A 55 LYS A 215 GLY A 219 SITE 2 BC8 6 THR A 221 HOH A2230 SITE 1 BC9 11 ALA A 245 ASN A 247 LYS A 248 TRP A 278 SITE 2 BC9 11 PRO A 450 ILE A 452 ASP A 456 EDO A1474 SITE 3 BC9 11 HOH A2258 HOH A2329 HOH A2461 SITE 1 CC1 8 ASP A 228 ASN A 230 GLY A 231 GLU A 232 SITE 2 CC1 8 ILE A 234 ASN A 235 HOH A2242 HOH A2244 SITE 1 CC2 14 TRP A 127 ASP A 130 ARG A 152 ARG A 154 SITE 2 CC2 14 GLY A 182 TYR A 233 ILE A 234 HIS A 236 SITE 3 CC2 14 ASP A 238 THR A 346 ALA A 351 HOH A2113 SITE 4 CC2 14 HOH A2355 HOH A2462 CRYST1 101.790 84.090 55.460 90.00 92.64 90.00 C 1 2 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 0.009824 0.000000 0.000453 0.00000 SCALE2 0.000000 0.011892 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018050 0.00000