HEADER TOXIN 22-OCT-14 3X0T TITLE CRYSTAL STRUCTURE OF PIRA COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PIRA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PARAHAEMOLYTICUS M0605; SOURCE 3 ORGANISM_TAXID: 1449358; SOURCE 4 GENE: AJ90_20630, PIRA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS JELLY ROLL FOLD, PORE FORMING TOXIN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR H.C.WANG,T.P.KO,A.H.J.WANG,C.F.LO REVDAT 2 24-AUG-22 3X0T 1 JRNL REMARK SEQADV REVDAT 1 26-AUG-15 3X0T 0 JRNL AUTH C.T.LEE,I.T.CHEN,Y.T.YANG,T.P.KO,Y.T.HUANG,J.Y.HUANG, JRNL AUTH 2 M.F.HUANG,S.J.LIN,C.Y.CHEN,S.S.LIN,S.S.LIN,D.V.LIGHTNER, JRNL AUTH 3 H.C.WANG,A.H.WANG,H.C.WANG,L.I.HOR,C.F.LO JRNL TITL THE OPPORTUNISTIC MARINE PATHOGEN VIBRIO PARAHAEMOLYTICUS JRNL TITL 2 BECOMES VIRULENT BY ACQUIRING A PLASMID THAT EXPRESSES A JRNL TITL 3 DEADLY TOXIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 10798 2015 JRNL REFN ESSN 1091-6490 JRNL PMID 26261348 JRNL DOI 10.1073/PNAS.1503129112 REMARK 2 REMARK 2 RESOLUTION. 1.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 74525 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) : 0.133 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3862 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) : 1.17 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5237 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 281 REMARK 3 BIN FREE R VALUE : 0.2520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1783 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 521 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.39000 REMARK 3 B22 (A**2) : 0.35000 REMARK 3 B33 (A**2) : -0.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.36000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.033 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.036 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.020 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.962 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1955 ; 0.022 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2674 ; 2.465 ; 1.904 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 243 ; 6.245 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 111 ;30.320 ;24.054 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 302 ;10.253 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;15.863 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 274 ; 0.147 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1591 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1158 ; 2.956 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1867 ; 3.849 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 797 ; 5.206 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 797 ; 7.126 ; 4.500 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): 1955 ; 3.143 ; 3.000 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3X0T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000097035. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78388 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.170 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.02300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.24200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30MM TRIS HCL, 100MM NACL, 1MM DTT, 5% REMARK 280 GLYCEROL, 20% PEG 3350, 0.2M KNO3, 15% ETHYLENE GLYCOL, PH 7.4, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 39.19850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.66900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.19850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.66900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 402 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 505 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 ASN A 3 REMARK 465 HIS A 116 REMARK 465 HIS A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ASN B 3 REMARK 465 LEU B 112 REMARK 465 GLU B 113 REMARK 465 HIS B 114 REMARK 465 HIS B 115 REMARK 465 HIS B 116 REMARK 465 HIS B 117 REMARK 465 HIS B 118 REMARK 465 HIS B 119 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 NH1 ARG A 84 O HOH A 331 1.19 REMARK 500 O HOH B 1159 O HOH B 1259 1.22 REMARK 500 O HOH A 317 O HOH A 508 1.44 REMARK 500 O HOH A 516 O HOH A 517 1.48 REMARK 500 O HOH B 1135 O HOH B 1241 1.51 REMARK 500 O HOH A 506 O HOH A 547 1.52 REMARK 500 O HOH A 518 O HOH A 544 1.53 REMARK 500 O HOH A 438 O HOH A 502 1.56 REMARK 500 O HOH B 1197 O HOH B 1263 1.57 REMARK 500 O HOH B 1130 O HOH B 1216 1.57 REMARK 500 ND2 ASN A 20 O HOH A 469 1.58 REMARK 500 O HOH A 412 O HOH A 547 1.62 REMARK 500 O HOH A 525 O HOH A 546 1.63 REMARK 500 O HOH A 423 O HOH B 1149 1.65 REMARK 500 ND1 HIS A 114 O HOH A 498 1.66 REMARK 500 O HOH A 396 O HOH A 523 1.66 REMARK 500 O HOH B 1138 O HOH B 1258 1.67 REMARK 500 O HOH A 334 O HOH A 535 1.69 REMARK 500 O HOH A 394 O HOH A 554 1.70 REMARK 500 O HOH A 451 O HOH A 535 1.71 REMARK 500 O HOH B 1131 O HOH B 1216 1.72 REMARK 500 O HOH B 1039 O HOH B 1104 1.74 REMARK 500 O HOH A 356 O HOH A 415 1.75 REMARK 500 O HOH B 1156 O HOH B 1236 1.75 REMARK 500 NE2 HIS A 111 O HOH A 494 1.75 REMARK 500 O HOH B 1095 O HOH B 1199 1.78 REMARK 500 O HOH B 1192 O HOH B 1206 1.78 REMARK 500 O HOH B 1109 O HOH B 1244 1.79 REMARK 500 O HOH B 1190 O HOH B 1258 1.80 REMARK 500 O HOH A 437 O HOH A 503 1.80 REMARK 500 O HOH B 1065 O HOH B 1245 1.81 REMARK 500 O HOH A 440 O HOH A 543 1.81 REMARK 500 O HOH B 1172 O HOH B 1173 1.81 REMARK 500 O HOH B 1158 O HOH B 1214 1.84 REMARK 500 O HOH A 383 O HOH A 416 1.85 REMARK 500 OD1 ASP B 10 O HOH B 1135 1.86 REMARK 500 O HOH A 469 O HOH A 512 1.90 REMARK 500 O HOH A 502 O HOH A 503 1.91 REMARK 500 O HOH B 1062 O HOH B 1253 1.93 REMARK 500 OD1 ASP A 42 O HOH A 494 1.93 REMARK 500 OE2 GLU B 18 O HOH B 1198 1.94 REMARK 500 O HOH B 1099 O HOH B 1209 1.95 REMARK 500 O HOH B 1103 O HOH B 1155 1.97 REMARK 500 O HOH B 1105 O HOH B 1236 1.98 REMARK 500 O HOH A 427 O HOH A 456 1.98 REMARK 500 O HOH A 494 O HOH A 543 1.98 REMARK 500 OG1 THR B 16 O HOH B 1112 1.99 REMARK 500 O HOH A 460 O HOH A 536 1.99 REMARK 500 O HOH B 1138 O HOH B 1160 2.00 REMARK 500 O1 NO3 B 905 O HOH B 1133 2.00 REMARK 500 REMARK 500 THIS ENTRY HAS 64 CLOSE CONTACTS 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 B 1259 O HOH B 1259 2655 1.37 REMARK 500 O HOH A 444 O HOH A 444 2655 1.60 REMARK 500 O HOH B 1217 O HOH B 1217 2655 1.65 REMARK 500 O HOH A 507 O HOH A 508 2655 1.66 REMARK 500 O HOH A 546 O HOH B 1233 4555 1.75 REMARK 500 O HOH A 555 O HOH B 1173 4656 1.78 REMARK 500 CD1 ILE A 5 O HOH B 1176 3555 1.85 REMARK 500 O HOH B 1090 O HOH B 1091 2655 1.87 REMARK 500 O HOH A 417 O HOH B 1200 4555 1.90 REMARK 500 O HOH A 511 O HOH B 1105 4656 1.91 REMARK 500 O HOH A 529 O HOH B 1254 3555 1.91 REMARK 500 O HOH A 524 O HOH B 1117 4555 1.95 REMARK 500 O HOH A 525 O HOH B 1233 4555 1.96 REMARK 500 O HOH A 396 O HOH A 491 2656 1.96 REMARK 500 O HOH A 418 O HOH B 1192 4555 1.96 REMARK 500 O HOH A 527 O HOH B 1235 4555 1.99 REMARK 500 O HOH A 473 O HOH A 474 2655 2.13 REMARK 500 OD2 ASP A 10 OD2 ASP A 10 2655 2.15 REMARK 500 O HOH A 458 O HOH B 1249 4656 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 25 CD GLU A 25 OE2 -0.096 REMARK 500 ARG A 84 CZ ARG A 84 NH2 -0.090 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 48 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP A 77 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 84 NH1 - CZ - NH2 ANGL. DEV. = -8.3 DEGREES REMARK 500 ARG A 84 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP A 86 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 GLU B 18 OE1 - CD - OE2 ANGL. DEV. = -8.9 DEGREES REMARK 500 ARG B 39 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP B 42 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP B 86 CB - CA - C ANGL. DEV. = -12.6 DEGREES REMARK 500 ASP B 86 CB - CG - OD2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG B 103 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 77 -6.33 69.78 REMARK 500 ASN A 87 118.36 -165.99 REMARK 500 ASP B 77 -8.00 74.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 905 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3X0U RELATED DB: PDB REMARK 900 STRUCTURE OF PIRB DBREF 3X0T A 1 111 UNP X7REN0 X7REN0_VIBPH 1 111 DBREF 3X0T B 1 111 UNP X7REN0 X7REN0_VIBPH 1 111 SEQADV 3X0T LEU A 112 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T GLU A 113 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T HIS A 114 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T HIS A 115 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T HIS A 116 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T HIS A 117 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T HIS A 118 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T HIS A 119 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T LEU B 112 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T GLU B 113 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T HIS B 114 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T HIS B 115 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T HIS B 116 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T HIS B 117 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T HIS B 118 UNP X7REN0 EXPRESSION TAG SEQADV 3X0T HIS B 119 UNP X7REN0 EXPRESSION TAG SEQRES 1 A 119 MET SER ASN ASN ILE LYS HIS GLU THR ASP TYR SER HIS SEQRES 2 A 119 ASP TRP THR VAL GLU PRO ASN GLY GLY VAL THR GLU VAL SEQRES 3 A 119 ASP SER LYS HIS THR PRO ILE ILE PRO GLU VAL GLY ARG SEQRES 4 A 119 SER VAL ASP ILE GLU ASN THR GLY ARG GLY GLU LEU THR SEQRES 5 A 119 ILE GLN TYR GLN TRP GLY ALA PRO PHE MET ALA GLY GLY SEQRES 6 A 119 TRP LYS VAL ALA LYS SER HIS VAL VAL GLN ARG ASP GLU SEQRES 7 A 119 THR TYR HIS LEU GLN ARG PRO ASP ASN ALA PHE TYR HIS SEQRES 8 A 119 GLN ARG ILE VAL VAL ILE ASN ASN GLY ALA SER ARG GLY SEQRES 9 A 119 PHE CYS THR ILE TYR TYR HIS LEU GLU HIS HIS HIS HIS SEQRES 10 A 119 HIS HIS SEQRES 1 B 119 MET SER ASN ASN ILE LYS HIS GLU THR ASP TYR SER HIS SEQRES 2 B 119 ASP TRP THR VAL GLU PRO ASN GLY GLY VAL THR GLU VAL SEQRES 3 B 119 ASP SER LYS HIS THR PRO ILE ILE PRO GLU VAL GLY ARG SEQRES 4 B 119 SER VAL ASP ILE GLU ASN THR GLY ARG GLY GLU LEU THR SEQRES 5 B 119 ILE GLN TYR GLN TRP GLY ALA PRO PHE MET ALA GLY GLY SEQRES 6 B 119 TRP LYS VAL ALA LYS SER HIS VAL VAL GLN ARG ASP GLU SEQRES 7 B 119 THR TYR HIS LEU GLN ARG PRO ASP ASN ALA PHE TYR HIS SEQRES 8 B 119 GLN ARG ILE VAL VAL ILE ASN ASN GLY ALA SER ARG GLY SEQRES 9 B 119 PHE CYS THR ILE TYR TYR HIS LEU GLU HIS HIS HIS HIS SEQRES 10 B 119 HIS HIS HET NO3 A 201 4 HET NO3 B 901 4 HET NO3 B 902 4 HET NO3 B 903 4 HET NO3 B 904 4 HET NO3 B 905 4 HETNAM NO3 NITRATE ION FORMUL 3 NO3 6(N O3 1-) FORMUL 9 HOH *521(H2 O) HELIX 1 1 ALA A 59 ALA A 63 5 5 HELIX 2 2 ALA B 59 ALA B 63 5 5 SHEET 1 A 4 TYR A 11 VAL A 17 0 SHEET 2 A 4 GLY A 104 TYR A 110 -1 O TYR A 110 N TYR A 11 SHEET 3 A 4 VAL A 41 ASN A 45 -1 N GLU A 44 O THR A 107 SHEET 4 A 4 THR A 79 LEU A 82 -1 O LEU A 82 N VAL A 41 SHEET 1 B 4 GLY A 22 HIS A 30 0 SHEET 2 B 4 HIS A 91 ASN A 98 -1 O ILE A 94 N VAL A 26 SHEET 3 B 4 LEU A 51 GLY A 58 -1 N THR A 52 O ILE A 97 SHEET 4 B 4 LYS A 67 VAL A 74 -1 O VAL A 74 N LEU A 51 SHEET 1 C 4 SER B 12 VAL B 17 0 SHEET 2 C 4 GLY B 104 TYR B 110 -1 O CYS B 106 N TRP B 15 SHEET 3 C 4 VAL B 41 ASN B 45 -1 N GLU B 44 O THR B 107 SHEET 4 C 4 THR B 79 LEU B 82 -1 O LEU B 82 N VAL B 41 SHEET 1 D 4 GLY B 22 HIS B 30 0 SHEET 2 D 4 HIS B 91 ASN B 98 -1 O VAL B 96 N THR B 24 SHEET 3 D 4 LEU B 51 GLY B 58 -1 N THR B 52 O ILE B 97 SHEET 4 D 4 LYS B 67 VAL B 74 -1 O VAL B 74 N LEU B 51 SITE 1 AC1 4 GLU A 36 VAL A 37 HOH A 527 ARG B 39 SITE 1 AC2 6 LYS A 67 VAL A 68 LYS B 70 SER B 71 SITE 2 AC2 6 HOH B1227 HOH B1228 SITE 1 AC3 6 GLN A 54 SER B 71 HIS B 72 VAL B 73 SITE 2 AC3 6 HOH B1002 HOH B1145 SITE 1 AC4 7 ARG A 39 LEU A 112 GLU A 113 GLU B 36 SITE 2 AC4 7 VAL B 37 HOH B1182 HOH B1183 SITE 1 AC5 4 ASP B 77 HIS B 81 HOH B1132 HOH B1175 SITE 1 AC6 9 TRP A 57 LYS A 67 ALA B 69 LYS B 70 SITE 2 AC6 9 PRO B 85 ASN B 87 HOH B1133 HOH B1181 SITE 3 AC6 9 HOH B1232 CRYST1 78.397 67.338 53.669 90.00 122.80 90.00 C 1 2 1 8 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 0.012756 0.000000 0.008220 0.00000 SCALE2 0.000000 0.014850 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022166 0.00000