HEADER HYDROLASE 18-JAN-13 4ITC TITLE CRYSTAL STRUCTURE ANALYSIS OF THE K1 CLEAVED ADHESIN DOMAIN OF LYS- TITLE 2 GINGIPAIN (KGP) FROM PORPHYROMONAS GINGIVALIS W83 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYS-GINGIPAIN W83; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: K1 CLEAVED ADHESIN DOMAIN, RESIDUES 982-1154; 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 STRAIN: W83; SOURCE 5 GENE: KGP, PRTK, PRTP; 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: PGEX-5X-3 KEYWDS BETA SANDWICH, CLEAVED ADHESIN FAMILY, LYS-GINGIPAIN, HEMAGGLUTININ KEYWDS 2 DOMAIN, CELL INVASION, CYSTEINE PROTEASE, CALCIUM BINDING, MEMBRANE KEYWDS 3 SURFACE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.A.GANUELAS,N.LI,N.HUNTER,C.A.COLLYER REVDAT 4 20-SEP-23 4ITC 1 REMARK LINK REVDAT 3 15-NOV-17 4ITC 1 REMARK REVDAT 2 15-JAN-14 4ITC 1 JRNL REVDAT 1 25-SEP-13 4ITC 0 JRNL AUTH L.A.GANUELAS,N.LI,P.YUN,N.HUNTER,C.A.COLLYER JRNL TITL THE LYSINE GINGIPAIN ADHESIN DOMAINS FROM PORPHYROMONAS JRNL TITL 2 GINGIVALIS INTERACT WITH ERYTHROCYTES AND ALBUMIN: JRNL TITL 3 STRUCTURES CORRELATE TO FUNCTION. JRNL REF EUR J MICROBIOL IMMUNOL (BP) V. 3 152 2013 JRNL REFN ISSN 2062-509X JRNL PMID 24265933 JRNL DOI 10.1556/EUJMI.3.2013.3.2 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 20886 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) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1000 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) : 1466 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.1860 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1244 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 123 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.07000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.075 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.076 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.254 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1360 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1182 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1863 ; 1.590 ; 1.940 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2712 ; 0.780 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 183 ; 7.546 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 59 ;33.375 ;25.254 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 176 ;10.156 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ; 9.081 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 199 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1670 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 350 ; 0.003 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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: CONJUGATE GRADIENT METHOD REMARK 4 REMARK 4 4ITC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95370 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22016 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 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) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.34200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.173 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: PDB ENTRY 3M1H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 MM KH2PO4, 20% (V/V) GLYCEROL, 16% REMARK 280 (W/V) PEG 8000, 1 M GUANIDINE HYDROCHLORIDE, PH 7.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 16.66050 REMARK 290 SMTRY3 2 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 1101 REMARK 465 VAL A 1102 REMARK 465 ARG A 1103 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 A1057 CG CD CE NZ REMARK 470 THR A1098 OG1 CG2 REMARK 470 LYS A1100 CG CD CE NZ REMARK 470 SER A1104 N CA CB OG REMARK 470 LYS A1106 CG CD CE NZ REMARK 470 ARG A1111 CG CD NE CZ NH1 NH2 REMARK 470 ILE A1112 CG1 CG2 CD1 REMARK 470 GLN A1113 CG CD OE1 NE2 REMARK 470 THR A1115 OG1 CG2 REMARK 470 GLU A1149 CG CD OE1 OE2 REMARK 470 LYS A1151 CG CD CE NZ REMARK 470 GLY A1154 C O 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 A1117 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A1144 CB - CG - OD1 ANGL. DEV. = 5.5 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 THR A1081 -98.08 -115.51 REMARK 500 THR A1081 -98.08 -125.09 REMARK 500 MET A1140 -107.93 -115.48 REMARK 500 PHE A1141 -99.73 -150.01 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 CA A1202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 988 O REMARK 620 2 GLU A 990 OE2 79.8 REMARK 620 3 SER A1022 OG 155.8 78.7 REMARK 620 4 GLY A1024 O 93.1 91.1 98.2 REMARK 620 5 ASP A1146 OD1 75.5 154.4 126.8 83.8 REMARK 620 6 ASP A1146 OD2 128.3 150.4 75.1 79.4 52.9 REMARK 620 7 GLU A1147 OE1 90.3 100.1 82.8 168.7 86.6 90.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A1001 OD1 REMARK 620 2 ASP A1003 OD1 85.2 REMARK 620 3 ASP A1003 OD2 88.5 50.9 REMARK 620 4 ASP A1005 OD1 89.8 119.9 69.1 REMARK 620 5 HIS A1007 O 93.7 157.4 151.7 82.7 REMARK 620 6 ASN A1043 OD1 99.9 76.3 125.7 162.1 81.7 REMARK 620 7 HOH A1301 O 166.3 97.4 82.8 77.2 89.0 93.8 REMARK 620 N 1 2 3 4 5 6 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 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAI A 1203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAI A 1204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAI A 1206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1207 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3M1H RELATED DB: PDB REMARK 900 K3 CLEAVED ADHESIN DOMAIN OF LYS-GINGIPAIN REMARK 900 RELATED ID: 3KM5 RELATED DB: PDB REMARK 900 K2 CLEAVED ADHESIN DOMAIN OF LYS-GINGIPAIN DBREF 4ITC A 982 1154 UNP Q51817 KGP83_PORGN 982 1154 SEQRES 1 A 173 GLY THR THR LEU SER GLU SER PHE GLU ASN GLY ILE PRO SEQRES 2 A 173 ALA SER TRP LYS THR ILE ASP ALA ASP GLY ASP GLY HIS SEQRES 3 A 173 GLY TRP LYS PRO GLY ASN ALA PRO GLY ILE ALA GLY TYR SEQRES 4 A 173 ASN SER ASN GLY CYS VAL TYR SER GLU SER PHE GLY LEU SEQRES 5 A 173 GLY GLY ILE GLY VAL LEU THR PRO ASP ASN TYR LEU ILE SEQRES 6 A 173 THR PRO ALA LEU ASP LEU PRO ASN GLY GLY LYS LEU THR SEQRES 7 A 173 PHE TRP VAL CYS ALA GLN ASP ALA ASN TYR ALA SER GLU SEQRES 8 A 173 HIS TYR ALA VAL TYR ALA SER SER THR GLY ASN ASP ALA SEQRES 9 A 173 SER ASN PHE THR ASN ALA LEU LEU GLU GLU THR ILE THR SEQRES 10 A 173 ALA LYS GLY VAL ARG SER PRO LYS ALA ILE ARG GLY ARG SEQRES 11 A 173 ILE GLN GLY THR TRP ARG GLN LYS THR VAL ASP LEU PRO SEQRES 12 A 173 ALA GLY THR LYS TYR VAL ALA PHE ARG HIS PHE GLN SER SEQRES 13 A 173 THR ASP MET PHE TYR ILE ASP LEU ASP GLU VAL GLU ILE SEQRES 14 A 173 LYS ALA ASN GLY HET CA A1201 1 HET CA A1202 1 HET GAI A1203 4 HET GAI A1204 4 HET GOL A1205 6 HET GAI A1206 4 HET GOL A1207 6 HETNAM CA CALCIUM ION HETNAM GAI GUANIDINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CA 2(CA 2+) FORMUL 4 GAI 3(C H5 N3) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 9 HOH *123(H2 O) HELIX 1 1 ASP A 1084 PHE A 1088 5 5 SHEET 1 A 4 THR A 984 GLU A 987 0 SHEET 2 A 4 TYR A1142 ALA A1152 -1 O VAL A1148 N GLU A 987 SHEET 3 A 4 GLY A1024 GLU A1029 -1 N VAL A1026 O LEU A1145 SHEET 4 A 4 LYS A1010 ASN A1013 -1 N GLY A1012 O CYS A1025 SHEET 1 B 4 THR A 984 GLU A 987 0 SHEET 2 B 4 TYR A1142 ALA A1152 -1 O VAL A1148 N GLU A 987 SHEET 3 B 4 GLY A1056 ALA A1064 -1 N CYS A1063 O ASP A1144 SHEET 4 B 4 ARG A1117 LEU A1123 -1 O LEU A1123 N GLY A1056 SHEET 1 C 5 LYS A 998 ASP A1001 0 SHEET 2 C 5 ASN A1043 ILE A1046 -1 O ILE A1046 N LYS A 998 SHEET 3 C 5 TYR A1129 HIS A1134 -1 O HIS A1134 N ASN A1043 SHEET 4 C 5 HIS A1073 SER A1079 -1 N ALA A1075 O ARG A1133 SHEET 5 C 5 ASN A1090 THR A1096 -1 O LEU A1092 N VAL A1076 SHEET 1 D 2 PHE A1031 GLY A1032 0 SHEET 2 D 2 GLY A1037 VAL A1038 -1 O GLY A1037 N GLY A1032 LINK O SER A 988 CA CA A1202 1555 1555 2.35 LINK OE2 GLU A 990 CA CA A1202 1555 1555 2.26 LINK OD1 ASP A1001 CA CA A1201 1555 1555 2.29 LINK OD1 ASP A1003 CA CA A1201 1555 1555 2.39 LINK OD2 ASP A1003 CA CA A1201 1555 1555 2.74 LINK OD1 ASP A1005 CA CA A1201 1555 1555 2.40 LINK O HIS A1007 CA CA A1201 1555 1555 2.33 LINK OG SER A1022 CA CA A1202 1555 1555 2.44 LINK O GLY A1024 CA CA A1202 1555 1555 2.32 LINK OD1 ASN A1043 CA CA A1201 1555 1555 2.39 LINK OD1 ASP A1146 CA CA A1202 1555 1555 2.43 LINK OD2 ASP A1146 CA CA A1202 1555 1555 2.48 LINK OE1 GLU A1147 CA CA A1202 1555 1555 2.40 LINK CA CA A1201 O HOH A1301 1555 1555 2.43 CISPEP 1 ALA A 1014 PRO A 1015 0 3.10 SITE 1 AC1 6 ASP A1001 ASP A1003 ASP A1005 HIS A1007 SITE 2 AC1 6 ASN A1043 HOH A1301 SITE 1 AC2 6 SER A 988 GLU A 990 SER A1022 GLY A1024 SITE 2 AC2 6 ASP A1146 GLU A1147 SITE 1 AC3 2 PRO A1053 ASN A1054 SITE 1 AC4 6 ASN A 991 PRO A 994 TYR A1069 ASP A1139 SITE 2 AC4 6 MET A1140 HOH A1340 SITE 1 AC5 7 SER A 996 SER A1071 GLN A1136 SER A1137 SITE 2 AC5 7 THR A1138 MET A1140 HOH A1345 SITE 1 AC6 6 ILE A 993 PRO A 994 TRP A 997 THR A 999 SITE 2 AC6 6 HOH A1304 HOH A1353 SITE 1 AC7 5 LEU A 985 SER A 986 GLU A 987 TRP A 997 SITE 2 AC7 5 SER A1071 CRYST1 34.034 33.321 67.245 90.00 93.96 90.00 P 1 21 1 2 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 0.029382 0.000000 0.002034 0.00000 SCALE2 0.000000 0.030011 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014907 0.00000