HEADER HYDROLASE 12-SEP-14 4RBM TITLE PORPHYROMONAS GINGIVALIS GINGIPAIN K (KGP) CATALYTIC AND TITLE 2 IMMUNOGLOBULIN SUPERFAMILY-LIKE DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYS-GINGIPAIN W83; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 229-683; COMPND 5 SYNONYM: LYSINE SPECIFIC CYSTEINE PROTEASE, LYSINE-SPECIFIC CYSTEINE COMPND 6 PROTEINASE, PORPHYPAIN, PRTK48, LYS-GINGIPAIN CATALYTIC SUBUNIT, 39 COMPND 7 KDA ADHESIN, PRTK39, 15 KDA ADHESIN, PRTK15, 44 KDA ADHESIN, PRTK44; COMPND 8 EC: 3.4.22.47; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYROMONAS GINGIVALIS; SOURCE 3 ORGANISM_TAXID: 837; SOURCE 4 GENE: KGP, PRTK, PRTP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALPHA/BETA-HYDROLASE, CYSTEINE PEPTIDASE, LYSINE-CONTAINING KEYWDS 2 SUBSTRATES, EXTRACELLULAR, SECRETED, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR I.DE DIEGO,F.VEILLARD,M.N.SZTUKOWSKA,T.GUEVARA,B.POTEMPA,A.POMOWSKI, AUTHOR 2 J.A.HUNTINGTON,J.POTEMPA,F.X.GOMIS-RUTH REVDAT 6 15-NOV-23 4RBM 1 LINK ATOM REVDAT 5 20-SEP-23 4RBM 1 REMARK SEQADV LINK REVDAT 4 22-NOV-17 4RBM 1 REMARK REVDAT 3 10-DEC-14 4RBM 1 JRNL REVDAT 2 15-OCT-14 4RBM 1 JRNL REVDAT 1 08-OCT-14 4RBM 0 JRNL AUTH I.DE DIEGO,F.VEILLARD,M.N.SZTUKOWSKA,T.GUEVARA,B.POTEMPA, JRNL AUTH 2 A.POMOWSKI,J.A.HUNTINGTON,J.POTEMPA,F.X.GOMIS-RUTH JRNL TITL STRUCTURE AND MECHANISM OF CYSTEINE PEPTIDASE GINGIPAIN K JRNL TITL 2 (KGP), A MAJOR VIRULENCE FACTOR OF PORPHYROMONAS GINGIVALIS JRNL TITL 3 IN PERIODONTITIS. JRNL REF J.BIOL.CHEM. V. 289 32291 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 25266723 JRNL DOI 10.1074/JBC.M114.602052 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.5 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 46299 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) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.660 REMARK 3 FREE R VALUE TEST SET COUNT : 767 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.79 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.56 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3213 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2206 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3166 REMARK 3 BIN R VALUE (WORKING SET) : 0.2202 REMARK 3 BIN FREE R VALUE : 0.2485 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 1.46 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 47 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 : 3520 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 533 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.81050 REMARK 3 B22 (A**2) : -0.58760 REMARK 3 B33 (A**2) : -0.22290 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.162 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.097 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3672 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4988 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1602 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 81 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 533 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3672 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 22 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 474 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 4210 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.00 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.49 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.55 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|229 - A|600 } REMARK 3 ORIGIN FOR THE GROUP (A): 35.0205 42.4190 19.7850 REMARK 3 T TENSOR REMARK 3 T11: -0.0348 T22: -0.0148 REMARK 3 T33: -0.0364 T12: 0.0020 REMARK 3 T13: -0.0007 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 0.4959 L22: 0.1857 REMARK 3 L33: 0.3452 L12: 0.0138 REMARK 3 L13: -0.0725 L23: -0.0085 REMARK 3 S TENSOR REMARK 3 S11: -0.0217 S12: -0.0207 S13: 0.0014 REMARK 3 S21: -0.0097 S22: 0.0087 S23: -0.0003 REMARK 3 S31: 0.0109 S32: -0.0022 S33: 0.0130 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|601 - A|680 } REMARK 3 ORIGIN FOR THE GROUP (A): 43.3500 69.3958 10.0328 REMARK 3 T TENSOR REMARK 3 T11: 0.1457 T22: -0.0331 REMARK 3 T33: 0.1975 T12: -0.0394 REMARK 3 T13: -0.0723 T23: 0.0322 REMARK 3 L TENSOR REMARK 3 L11: 7.1227 L22: 1.9354 REMARK 3 L33: 2.4156 L12: 2.1577 REMARK 3 L13: 2.0924 L23: 0.3204 REMARK 3 S TENSOR REMARK 3 S11: -0.5162 S12: 0.2375 S13: 0.9871 REMARK 3 S21: -0.2909 S22: 0.1000 S23: 0.0395 REMARK 3 S31: -0.5519 S32: 0.2217 S33: 0.4161 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4RBM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000087143. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46309 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 45.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.69200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: PDB ENTRY 1CVR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE BEST CRYSTALS WERE OBTAINED AT 20C REMARK 280 WITH PROTEIN SOLUTION (AT 5.7MG/ML IN 5MM TRIS HCL, PH 7.4, 0.02% REMARK 280 SODIUM AZIDE) AND 22% POLYETHYLENE GLYCOL 8000, 0.1M SODIUM REMARK 280 CACODYLATE, PH 6.5, 0.2M CALCIUM ACETATE AS RESERVOIR SOLUTION REMARK 280 FROM 2:1 UL DROPS, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K 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 28.32000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.75000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.40500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.75000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.32000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.40500 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 GLY A 681 REMARK 465 GLU A 682 REMARK 465 PRO A 683 REMARK 465 HIS A 684 REMARK 465 HIS A 685 REMARK 465 HIS A 686 REMARK 465 HIS A 687 REMARK 465 HIS A 688 REMARK 465 HIS A 689 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 VAL A 395 -40.31 -131.89 REMARK 500 TYR A 407 -53.75 -136.17 REMARK 500 THR A 426 124.35 -39.82 REMARK 500 ALA A 443 -142.55 164.78 REMARK 500 ILE A 478 12.00 47.26 REMARK 500 ILE A 576 -33.85 -149.61 REMARK 500 ALA A 598 -149.66 67.82 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 HIS A 707 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 CA A 701 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 313 OD1 REMARK 620 2 ASP A 313 OD2 51.5 REMARK 620 3 PHE A 482 O 81.8 133.3 REMARK 620 4 GLU A 491 OE2 74.0 76.6 91.1 REMARK 620 5 GLU A 491 OE1 125.6 109.2 96.3 51.6 REMARK 620 6 HOH A 816 O 154.1 145.9 78.1 122.4 73.3 REMARK 620 7 HOH A 850 O 78.0 89.1 81.0 151.7 155.9 82.7 REMARK 620 8 HOH A 853 O 120.9 72.3 150.1 112.8 85.8 74.0 85.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 702 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 337 OD1 REMARK 620 2 ASP A 339 OD1 87.3 REMARK 620 3 PHE A 341 O 164.3 89.2 REMARK 620 4 GLU A 343 OE1 97.9 150.3 92.7 REMARK 620 5 GLU A 343 OE2 82.1 155.9 95.1 53.3 REMARK 620 6 HOH A 836 O 80.9 80.8 83.4 128.8 76.2 REMARK 620 7 HOH A 874 O 95.7 70.9 97.7 79.5 131.6 151.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 705 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 379 OE2 REMARK 620 2 GLU A 379 OE1 52.7 REMARK 620 3 HIS A 707 NE2 118.5 84.6 REMARK 620 4 ACT A 708 OXT 106.4 76.3 102.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 703 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 402 OH REMARK 620 2 VAL A 521 O 92.7 REMARK 620 3 THR A 536 OG1 93.0 97.8 REMARK 620 4 SER A 537 O 163.7 96.9 98.6 REMARK 620 5 ASP A 542 OD2 77.7 88.1 169.2 89.5 REMARK 620 6 HOH A1275 O 89.9 176.3 84.8 79.9 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 706 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 415 O REMARK 620 2 HOH A 891 O 77.7 REMARK 620 3 HOH A 904 O 74.1 112.7 REMARK 620 4 HOH A1060 O 101.6 83.0 161.8 REMARK 620 5 HOH A1204 O 155.2 80.2 104.6 86.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 704 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 543 O REMARK 620 2 THR A 544 O 76.6 REMARK 620 3 LEU A 546 O 102.5 96.0 REMARK 620 4 SER A 549 O 91.6 168.0 85.0 REMARK 620 5 TYR A 550 O 82.0 100.1 163.9 79.3 REMARK 620 6 ASN A 551 OD1 169.1 106.9 87.5 85.0 87.3 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 CA A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HIS A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 708 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 709 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI A 710 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI A 711 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI A 712 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 713 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 714 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 715 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 716 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CKC A 717 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IEF RELATED DB: PDB REMARK 900 GINGIPAIN R2 (RGPB) PRO, CATALYTIC AND IMMUNOGLOBULIN SUPERFAMILY- REMARK 900 LIKE DOMAINS REMARK 900 RELATED ID: 1CVR RELATED DB: PDB REMARK 900 GINGIPAIN R2 (RGPB) CATALYTIC AND IMMUNOGLOBULIN SUPERFAMILY-LIKE REMARK 900 DOMAINS DBREF 4RBM A 229 683 UNP Q51817 KGP83_PORGN 229 683 SEQADV 4RBM HIS A 684 UNP Q51817 EXPRESSION TAG SEQADV 4RBM HIS A 685 UNP Q51817 EXPRESSION TAG SEQADV 4RBM HIS A 686 UNP Q51817 EXPRESSION TAG SEQADV 4RBM HIS A 687 UNP Q51817 EXPRESSION TAG SEQADV 4RBM HIS A 688 UNP Q51817 EXPRESSION TAG SEQADV 4RBM HIS A 689 UNP Q51817 EXPRESSION TAG SEQRES 1 A 461 ASP VAL TYR THR ASP HIS GLY ASP LEU TYR ASN THR PRO SEQRES 2 A 461 VAL ARG MET LEU VAL VAL ALA GLY ALA LYS PHE LYS GLU SEQRES 3 A 461 ALA LEU LYS PRO TRP LEU THR TRP LYS ALA GLN LYS GLY SEQRES 4 A 461 PHE TYR LEU ASP VAL HIS TYR THR ASP GLU ALA GLU VAL SEQRES 5 A 461 GLY THR THR ASN ALA SER ILE LYS ALA PHE ILE HIS LYS SEQRES 6 A 461 LYS TYR ASN ASP GLY LEU ALA ALA SER ALA ALA PRO VAL SEQRES 7 A 461 PHE LEU ALA LEU VAL GLY ASP THR ASP VAL ILE SER GLY SEQRES 8 A 461 GLU LYS GLY LYS LYS THR LYS LYS VAL THR ASP LEU TYR SEQRES 9 A 461 TYR SER ALA VAL ASP GLY ASP TYR PHE PRO GLU MET TYR SEQRES 10 A 461 THR PHE ARG MET SER ALA SER SER PRO GLU GLU LEU THR SEQRES 11 A 461 ASN ILE ILE ASP LYS VAL LEU MET TYR GLU LYS ALA THR SEQRES 12 A 461 MET PRO ASP LYS SER TYR LEU GLU LYS VAL LEU LEU ILE SEQRES 13 A 461 ALA GLY ALA ASP TYR SER TRP ASN SER GLN VAL GLY GLN SEQRES 14 A 461 PRO THR ILE LYS TYR GLY MET GLN TYR TYR TYR ASN GLN SEQRES 15 A 461 GLU HIS GLY TYR THR ASP VAL TYR ASN TYR LEU LYS ALA SEQRES 16 A 461 PRO TYR THR GLY CYS TYR SER HIS LEU ASN THR GLY VAL SEQRES 17 A 461 SER PHE ALA ASN TYR THR ALA HIS GLY SER GLU THR ALA SEQRES 18 A 461 TRP ALA ASP PRO LEU LEU THR THR SER GLN LEU LYS ALA SEQRES 19 A 461 LEU THR ASN LYS ASP LYS TYR PHE LEU ALA ILE GLY ASN SEQRES 20 A 461 CYS CYS ILE THR ALA GLN PHE ASP TYR VAL GLN PRO CYS SEQRES 21 A 461 PHE GLY GLU VAL ILE THR ARG VAL LYS GLU LYS GLY ALA SEQRES 22 A 461 TYR ALA TYR ILE GLY SER SER PRO ASN SER TYR TRP GLY SEQRES 23 A 461 GLU ASP TYR TYR TRP SER VAL GLY ALA ASN ALA VAL PHE SEQRES 24 A 461 GLY VAL GLN PRO THR PHE GLU GLY THR SER MET GLY SER SEQRES 25 A 461 TYR ASP ALA THR PHE LEU GLU ASP SER TYR ASN THR VAL SEQRES 26 A 461 ASN SER ILE MET TRP ALA GLY ASN LEU ALA ALA THR HIS SEQRES 27 A 461 ALA GLY ASN ILE GLY ASN ILE THR HIS ILE GLY ALA HIS SEQRES 28 A 461 TYR TYR TRP GLU ALA TYR HIS VAL LEU GLY ASP GLY SER SEQRES 29 A 461 VAL MET PRO TYR ARG ALA MET PRO LYS THR ASN THR TYR SEQRES 30 A 461 THR LEU PRO ALA SER LEU PRO GLN ASN GLN ALA SER TYR SEQRES 31 A 461 SER ILE GLN ALA SER ALA GLY SER TYR VAL ALA ILE SER SEQRES 32 A 461 LYS ASP GLY VAL LEU TYR GLY THR GLY VAL ALA ASN ALA SEQRES 33 A 461 SER GLY VAL ALA THR VAL SER MET THR LYS GLN ILE THR SEQRES 34 A 461 GLU ASN GLY ASN TYR ASP VAL VAL ILE THR ARG SER ASN SEQRES 35 A 461 TYR LEU PRO VAL ILE LYS GLN ILE GLN VAL GLY GLU PRO SEQRES 36 A 461 HIS HIS HIS HIS HIS HIS HET CA A 701 1 HET CA A 702 1 HET NA A 703 1 HET NA A 704 1 HET NI A 705 1 HET NA A 706 1 HET HIS A 707 10 HET ACT A 708 4 HET ACT A 709 4 HET AZI A 710 3 HET AZI A 711 3 HET AZI A 712 3 HET GOL A 713 6 HET GOL A 714 6 HET GOL A 715 6 HET GOL A 716 6 HET CKC A 717 10 HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM NI NICKEL (II) ION HETNAM HIS HISTIDINE HETNAM ACT ACETATE ION HETNAM AZI AZIDE ION HETNAM GOL GLYCEROL HETNAM CKC (3S)-3,7-DIAMINOHEPTAN-2-ONE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CA 2(CA 2+) FORMUL 4 NA 3(NA 1+) FORMUL 6 NI NI 2+ FORMUL 8 HIS C6 H10 N3 O2 1+ FORMUL 9 ACT 2(C2 H3 O2 1-) FORMUL 11 AZI 3(N3 1-) FORMUL 14 GOL 4(C3 H8 O3) FORMUL 18 CKC C7 H16 N2 O FORMUL 19 HOH *533(H2 O) HELIX 1 1 ASP A 229 HIS A 234 1 6 HELIX 2 2 PHE A 252 LYS A 266 1 15 HELIX 3 3 THR A 283 ALA A 301 1 19 HELIX 4 4 ASP A 330 ALA A 335 1 6 HELIX 5 5 SER A 353 LYS A 369 1 17 HELIX 6 6 ASP A 374 LEU A 378 5 5 HELIX 7 7 SER A 390 VAL A 395 1 6 HELIX 8 8 VAL A 395 TYR A 407 1 13 HELIX 9 9 ASN A 409 GLY A 413 5 5 HELIX 10 10 TYR A 429 GLY A 435 1 7 HELIX 11 11 THR A 457 ALA A 462 1 6 HELIX 12 12 CYS A 488 VAL A 496 1 9 HELIX 13 13 TYR A 512 GLY A 522 1 11 HELIX 14 14 GLY A 539 LEU A 546 1 8 HELIX 15 15 THR A 552 ILE A 570 1 19 HELIX 16 16 GLY A 577 ALA A 584 1 8 SHEET 1 A 4 PHE A 268 TYR A 274 0 SHEET 2 A 4 VAL A 242 ALA A 248 1 N VAL A 246 O HIS A 273 SHEET 3 A 4 PHE A 307 VAL A 311 1 O ALA A 309 N LEU A 245 SHEET 4 A 4 TYR A 345 MET A 349 1 O PHE A 347 N LEU A 310 SHEET 1 B 2 GLU A 320 LYS A 321 0 SHEET 2 B 2 VAL A 328 THR A 329 -1 O THR A 329 N GLU A 320 SHEET 1 C 6 ASP A 416 TYR A 420 0 SHEET 2 C 6 LYS A 380 ALA A 385 1 N ALA A 385 O TYR A 420 SHEET 3 C 6 PHE A 438 THR A 442 1 O ASN A 440 N ILE A 384 SHEET 4 C 6 PHE A 470 ASN A 475 1 O ASN A 475 N TYR A 441 SHEET 5 C 6 ALA A 501 SER A 507 1 O ILE A 505 N GLY A 474 SHEET 6 C 6 TYR A 585 GLY A 589 -1 O LEU A 588 N TYR A 504 SHEET 1 D 3 GLY A 445 SER A 446 0 SHEET 2 D 3 ALA A 449 TRP A 450 -1 O ALA A 449 N SER A 446 SHEET 3 D 3 LEU A 455 THR A 456 -1 O LEU A 455 N TRP A 450 SHEET 1 E 7 TYR A 605 THR A 606 0 SHEET 2 E 7 SER A 617 ALA A 622 -1 O GLN A 621 N THR A 606 SHEET 3 E 7 VAL A 647 MET A 652 -1 O ALA A 648 N ILE A 620 SHEET 4 E 7 VAL A 635 VAL A 641 -1 N THR A 639 O SER A 651 SHEET 5 E 7 TYR A 627 LYS A 632 -1 N VAL A 628 O GLY A 640 SHEET 6 E 7 GLY A 660 THR A 667 -1 O THR A 667 N TYR A 627 SHEET 7 E 7 VAL A 674 VAL A 680 -1 O LYS A 676 N VAL A 664 LINK SG CYS A 477 CAK CKC A 717 1555 1555 1.84 LINK OD1 ASP A 313 CA CA A 701 1555 1555 2.51 LINK OD2 ASP A 313 CA CA A 701 1555 1555 2.55 LINK OD1 ASP A 337 CA CA A 702 1555 1555 2.29 LINK OD1 ASP A 339 CA CA A 702 1555 1555 2.34 LINK O PHE A 341 CA CA A 702 1555 1555 2.31 LINK OE1 GLU A 343 CA CA A 702 1555 1555 2.32 LINK OE2 GLU A 343 CA CA A 702 1555 1555 2.55 LINK OE2 GLU A 379 NI NI A 705 1555 1555 2.01 LINK OE1 GLU A 379 NI NI A 705 1555 1555 2.74 LINK OH TYR A 402 NA NA A 703 1555 1555 2.59 LINK O THR A 415 NA NA A 706 1555 1555 2.32 LINK O PHE A 482 CA CA A 701 1555 1555 2.33 LINK OE2 GLU A 491 CA CA A 701 1555 1555 2.44 LINK OE1 GLU A 491 CA CA A 701 1555 1555 2.60 LINK O VAL A 521 NA NA A 703 1555 1555 2.31 LINK OG1 THR A 536 NA NA A 703 1555 1555 2.37 LINK O SER A 537 NA NA A 703 1555 1555 2.40 LINK OD2 ASP A 542 NA NA A 703 1555 1555 2.35 LINK O ALA A 543 NA NA A 704 1555 1555 2.69 LINK O THR A 544 NA NA A 704 1555 1555 2.46 LINK O LEU A 546 NA NA A 704 1555 1555 2.36 LINK O SER A 549 NA NA A 704 1555 1555 2.36 LINK O TYR A 550 NA NA A 704 1555 1555 2.52 LINK OD1 ASN A 551 NA NA A 704 1555 1555 2.45 LINK CA CA A 701 O HOH A 816 1555 1555 2.51 LINK CA CA A 701 O HOH A 850 1555 1555 2.50 LINK CA CA A 701 O HOH A 853 1555 1555 2.50 LINK CA CA A 702 O HOH A 836 1555 1555 2.44 LINK CA CA A 702 O HOH A 874 1555 1555 2.41 LINK NA NA A 703 O HOH A1275 1555 1555 2.43 LINK NI NI A 705 NE2 HIS A 707 1555 1555 1.98 LINK NI NI A 705 OXT ACT A 708 1555 1555 2.07 LINK NA NA A 706 O HOH A 891 1555 1555 2.91 LINK NA NA A 706 O HOH A 904 1555 1555 2.25 LINK NA NA A 706 O HOH A1060 1555 1555 2.24 LINK NA NA A 706 O HOH A1204 1555 1555 2.37 CISPEP 1 THR A 240 PRO A 241 0 -5.45 CISPEP 2 ALA A 423 PRO A 424 0 5.68 CISPEP 3 ASP A 452 PRO A 453 0 4.20 SITE 1 AC1 6 ASP A 313 PHE A 482 GLU A 491 HOH A 816 SITE 2 AC1 6 HOH A 850 HOH A 853 SITE 1 AC2 6 ASP A 337 ASP A 339 PHE A 341 GLU A 343 SITE 2 AC2 6 HOH A 836 HOH A 874 SITE 1 AC3 6 TYR A 402 VAL A 521 THR A 536 SER A 537 SITE 2 AC3 6 ASP A 542 HOH A1275 SITE 1 AC4 6 ALA A 543 THR A 544 LEU A 546 SER A 549 SITE 2 AC4 6 TYR A 550 ASN A 551 SITE 1 AC5 4 GLU A 355 GLU A 379 HIS A 707 ACT A 708 SITE 1 AC6 6 THR A 415 GLU A 498 HOH A 891 HOH A 904 SITE 2 AC6 6 HOH A1060 HOH A1204 SITE 1 AC7 5 GLU A 355 GLU A 379 NI A 705 ACT A 708 SITE 2 AC7 5 HOH A 992 SITE 1 AC8 7 GLU A 355 GLU A 379 LYS A 497 NI A 705 SITE 2 AC8 7 HIS A 707 HOH A1313 HOH A1315 SITE 1 AC9 5 GLU A 356 ARG A 495 HOH A 881 HOH A1066 SITE 2 AC9 5 HOH A1134 SITE 1 BC1 7 HIS A 234 ASP A 339 TYR A 389 SER A 390 SITE 2 BC1 7 AZI A 712 HOH A1221 HOH A1251 SITE 1 BC2 5 HIS A 234 GLY A 235 LEU A 237 TRP A 558 SITE 2 BC2 5 HOH A1327 SITE 1 BC3 6 ASP A 233 HIS A 234 ASP A 388 AZI A 710 SITE 2 BC3 6 HOH A1001 HOH A1221 SITE 1 BC4 4 LYS A 288 GLU A 320 TYR A 332 HOH A1097 SITE 1 BC5 4 TYR A 418 ASN A 419 TYR A 420 GOL A 716 SITE 1 BC6 6 TYR A 420 LEU A 421 LYS A 422 PRO A 424 SITE 2 BC6 6 HOH A1076 HOH A1140 SITE 1 BC7 8 ASP A 416 VAL A 417 TYR A 418 LYS A 466 SITE 2 BC7 8 GOL A 714 HOH A 904 HOH A1162 HOH A1317 SITE 1 BC8 14 ASP A 229 THR A 232 THR A 442 ALA A 443 SITE 2 BC8 14 HIS A 444 GLY A 445 ASN A 475 CYS A 477 SITE 3 BC8 14 SER A 511 TRP A 513 ASP A 516 HOH A 929 SITE 4 BC8 14 HOH A1045 HOH A1142 CRYST1 56.640 58.810 135.500 90.00 90.00 90.00 P 21 21 21 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 0.017655 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007380 0.00000