HEADER TOXIN 22-OCT-14 3X0U TITLE CRYSTAL STRUCTURE OF PIRB COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PIRB; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PARAHAEMOLYTICUS M0605; SOURCE 3 ORGANISM_TAXID: 1449358; SOURCE 4 GENE: AJ90_20625, PIRB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SEVEN-HELIX BUNDLE, BETA BARREL, PORE-FORMING TOXIN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR H.C.WANG,T.P.KO,A.H.J.WANG,C.F.LO REVDAT 3 24-AUG-22 3X0U 1 JRNL SEQADV REVDAT 2 22-NOV-17 3X0U 1 REMARK REVDAT 1 26-AUG-15 3X0U 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. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 94329 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 : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4891 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6563 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 346 REMARK 3 BIN FREE R VALUE : 0.2460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6854 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 995 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.10000 REMARK 3 B33 (A**2) : 0.08000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.091 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.090 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.915 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7027 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6404 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9542 ; 1.731 ; 1.938 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14742 ; 0.870 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 844 ; 6.287 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 378 ;34.209 ;24.974 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1152 ;12.096 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;16.019 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1011 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8100 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1688 ; 0.001 ; 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): 3382 ; 1.943 ; 1.582 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3381 ; 1.942 ; 1.580 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4224 ; 3.106 ; 2.358 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4225 ; 3.105 ; 2.360 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3644 ; 2.851 ; 1.915 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3645 ; 2.850 ; 1.917 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5319 ; 4.465 ; 2.759 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 9187 ; 7.093 ;14.837 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8660 ; 6.670 ;13.922 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3X0U 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_1000097036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 99668 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.50900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 (%): 44.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM TRIS, 300MM NACL, 20% 1,4 REMARK 280 -BUTANEDIOL, 0.1M NA-ACETATE, 15% 2,3-BUTANEDIOL, PH 4.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 58.55200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.55200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 60.44850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.30900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.44850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.30900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.55200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.44850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.30900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.55200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.44850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 64.30900 REMARK 290 SMTRY3 8 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 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 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 781 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 887 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 943 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1016 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 665 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 THR A 2 REMARK 465 ASN A 3 REMARK 465 GLU A 4 REMARK 465 TYR A 5 REMARK 465 VAL A 6 REMARK 465 VAL A 7 REMARK 465 THR A 8 REMARK 465 MET A 9 REMARK 465 SER A 10 REMARK 465 SER A 11 REMARK 465 GLU A 437 REMARK 465 LYS A 438 REMARK 465 LEU A 439 REMARK 465 GLU A 440 REMARK 465 HIS A 441 REMARK 465 HIS A 442 REMARK 465 HIS A 443 REMARK 465 HIS A 444 REMARK 465 HIS A 445 REMARK 465 HIS A 446 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ASN B 3 REMARK 465 GLU B 4 REMARK 465 TYR B 5 REMARK 465 VAL B 6 REMARK 465 VAL B 7 REMARK 465 THR B 8 REMARK 465 MET B 9 REMARK 465 SER B 10 REMARK 465 SER B 11 REMARK 465 LEU B 12 REMARK 465 THR B 13 REMARK 465 GLU B 14 REMARK 465 PHE B 15 REMARK 465 ASN B 16 REMARK 465 PRO B 17 REMARK 465 ASN B 18 REMARK 465 ASN B 19 REMARK 465 ALA B 20 REMARK 465 HIS B 442 REMARK 465 HIS B 443 REMARK 465 HIS B 444 REMARK 465 HIS B 445 REMARK 465 HIS B 446 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 501 O HOH A 794 1.64 REMARK 500 O HOH B 501 O HOH B 721 1.69 REMARK 500 O HOH B 653 O HOH B 731 1.73 REMARK 500 O HOH A 581 O HOH A 999 1.78 REMARK 500 O HOH A 690 O HOH A 791 1.80 REMARK 500 O HOH A 558 O HOH A 941 1.84 REMARK 500 O HOH A 705 O HOH A 997 1.84 REMARK 500 O HOH B 569 O HOH B 723 1.84 REMARK 500 O HOH B 569 O HOH B 812 1.93 REMARK 500 O HOH A 705 O HOH A 786 1.97 REMARK 500 OH TYR A 35 O HOH A 858 1.98 REMARK 500 O HOH A 944 O HOH A 947 1.99 REMARK 500 OE2 GLU B 105 O HOH B 832 2.00 REMARK 500 O HOH A 704 O HOH A 885 2.01 REMARK 500 O HOH B 680 O HOH B 826 2.03 REMARK 500 OD1 ASP B 417 O HOH B 845 2.04 REMARK 500 O HOH B 694 O HOH B 720 2.04 REMARK 500 OD1 ASP A 203 O HOH A 845 2.06 REMARK 500 O HOH B 578 O HOH B 976 2.06 REMARK 500 O HOH A 692 O HOH A 1011 2.06 REMARK 500 O HOH B 720 O HOH B 920 2.06 REMARK 500 O HOH A 708 O HOH A 709 2.07 REMARK 500 O HOH A 708 O HOH A 794 2.08 REMARK 500 O HOH A 658 O HOH A 688 2.09 REMARK 500 O HOH A 630 O HOH A 917 2.13 REMARK 500 NH2 ARG A 398 O HOH A 864 2.14 REMARK 500 O HOH B 752 O HOH B 753 2.14 REMARK 500 O HOH B 713 O HOH B 735 2.17 REMARK 500 OE1 GLU A 371 O HOH A 735 2.17 REMARK 500 O HOH A 614 O HOH A 690 2.19 REMARK 500 O HOH A 1004 O HOH B 925 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 653 O HOH B 653 3655 1.59 REMARK 500 O HOH B 945 O HOH B 945 3655 1.74 REMARK 500 O HOH A 905 O HOH A 905 4556 1.91 REMARK 500 O HOH A 822 O HOH B 803 7545 2.05 REMARK 500 O HOH B 626 O HOH B 638 3655 2.07 REMARK 500 O HOH B 626 O HOH B 626 3655 2.17 REMARK 500 O HOH B 654 O HOH B 655 3655 2.18 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 307 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 307 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 327 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 398 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 398 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG B 236 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 307 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B 324 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP B 347 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 GLU B 402 OE1 - CD - OE2 ANGL. DEV. = 9.2 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 ASN A 68 135.81 65.93 REMARK 500 GLU A 69 -129.05 63.33 REMARK 500 PRO A 70 126.40 -35.56 REMARK 500 SER A 101 -83.35 -115.05 REMARK 500 TYR A 136 -52.98 -121.52 REMARK 500 TYR A 321 -3.40 76.42 REMARK 500 ASP A 383 -12.40 82.28 REMARK 500 SER B 101 -85.24 -108.98 REMARK 500 PRO B 277 125.24 -39.27 REMARK 500 HIS B 320 57.62 37.86 REMARK 500 ASP B 383 -0.24 76.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 69 PRO A 70 -147.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3X0T RELATED DB: PDB REMARK 900 STRUCTURE OF PIRA DBREF 3X0U A 1 438 UNP X7RH70 X7RH70_VIBPH 1 438 DBREF 3X0U B 1 438 UNP X7RH70 X7RH70_VIBPH 1 438 SEQADV 3X0U LEU A 439 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U GLU A 440 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U HIS A 441 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U HIS A 442 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U HIS A 443 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U HIS A 444 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U HIS A 445 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U HIS A 446 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U LEU B 439 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U GLU B 440 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U HIS B 441 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U HIS B 442 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U HIS B 443 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U HIS B 444 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U HIS B 445 UNP X7RH70 EXPRESSION TAG SEQADV 3X0U HIS B 446 UNP X7RH70 EXPRESSION TAG SEQRES 1 A 446 MET THR ASN GLU TYR VAL VAL THR MET SER SER LEU THR SEQRES 2 A 446 GLU PHE ASN PRO ASN ASN ALA ARG LYS SER TYR LEU PHE SEQRES 3 A 446 ASP ASN TYR GLU VAL ASP PRO ASN TYR ALA PHE LYS ALA SEQRES 4 A 446 MET VAL SER PHE GLY LEU SER ASN ILE PRO TYR ALA GLY SEQRES 5 A 446 GLY PHE LEU SER THR LEU TRP ASN ILE PHE TRP PRO ASN SEQRES 6 A 446 THR PRO ASN GLU PRO ASP ILE GLU ASN ILE TRP GLU GLN SEQRES 7 A 446 LEU ARG ASP ARG ILE GLN ASP LEU VAL ASP GLU SER ILE SEQRES 8 A 446 ILE ASP ALA ILE ASN GLY ILE LEU ASP SER LYS ILE LYS SEQRES 9 A 446 GLU THR ARG ASP LYS ILE GLN ASP ILE ASN GLU THR ILE SEQRES 10 A 446 GLU ASN PHE GLY TYR ALA ALA ALA LYS ASP ASP TYR ILE SEQRES 11 A 446 GLY LEU VAL THR HIS TYR LEU ILE GLY LEU GLU GLU ASN SEQRES 12 A 446 PHE LYS ARG GLU LEU ASP GLY ASP GLU TRP LEU GLY TYR SEQRES 13 A 446 ALA ILE LEU PRO LEU LEU ALA THR THR VAL SER LEU GLN SEQRES 14 A 446 ILE THR TYR MET ALA CYS GLY LEU ASP TYR LYS ASP GLU SEQRES 15 A 446 PHE GLY PHE THR ASP SER ASP VAL HIS LYS LEU THR ARG SEQRES 16 A 446 ASN ILE ASP LYS LEU TYR ASP ASP VAL SER SER TYR ILE SEQRES 17 A 446 THR GLU LEU ALA ALA TRP ALA ASP ASN ASP SER TYR ASN SEQRES 18 A 446 ASN ALA ASN GLN ASP ASN VAL TYR ASP GLU VAL MET GLY SEQRES 19 A 446 ALA ARG SER TRP CYS THR VAL HIS GLY PHE GLU HIS MET SEQRES 20 A 446 LEU ILE TRP GLN LYS ILE LYS GLU LEU LYS LYS VAL ASP SEQRES 21 A 446 VAL PHE VAL HIS SER ASN LEU ILE SER TYR SER PRO ALA SEQRES 22 A 446 VAL GLY PHE PRO SER GLY ASN PHE ASN TYR ILE ALA THR SEQRES 23 A 446 GLY THR GLU ASP GLU ILE PRO GLN PRO LEU LYS PRO ASN SEQRES 24 A 446 MET PHE GLY GLU ARG ARG ASN ARG ILE VAL LYS ILE GLU SEQRES 25 A 446 SER TRP ASN SER ILE GLU ILE HIS TYR TYR ASN ARG VAL SEQRES 26 A 446 GLY ARG LEU LYS LEU THR TYR GLU ASN GLY GLU VAL VAL SEQRES 27 A 446 GLU LEU GLY LYS ALA HIS LYS TYR ASP GLU HIS TYR GLN SEQRES 28 A 446 SER ILE GLU LEU ASN GLY ALA TYR ILE LYS TYR VAL ASP SEQRES 29 A 446 VAL ILE ALA ASN GLY PRO GLU ALA ILE ASP ARG ILE VAL SEQRES 30 A 446 PHE HIS PHE SER ASP ASP ARG THR PHE VAL VAL GLY GLU SEQRES 31 A 446 ASN SER GLY LYS PRO SER VAL ARG LEU GLN LEU GLU GLY SEQRES 32 A 446 HIS PHE ILE CYS GLY MET LEU ALA ASP GLN GLU GLY SER SEQRES 33 A 446 ASP LYS VAL ALA ALA PHE SER VAL ALA TYR GLU LEU PHE SEQRES 34 A 446 HIS PRO ASP GLU PHE GLY THR GLU LYS LEU GLU HIS HIS SEQRES 35 A 446 HIS HIS HIS HIS SEQRES 1 B 446 MET THR ASN GLU TYR VAL VAL THR MET SER SER LEU THR SEQRES 2 B 446 GLU PHE ASN PRO ASN ASN ALA ARG LYS SER TYR LEU PHE SEQRES 3 B 446 ASP ASN TYR GLU VAL ASP PRO ASN TYR ALA PHE LYS ALA SEQRES 4 B 446 MET VAL SER PHE GLY LEU SER ASN ILE PRO TYR ALA GLY SEQRES 5 B 446 GLY PHE LEU SER THR LEU TRP ASN ILE PHE TRP PRO ASN SEQRES 6 B 446 THR PRO ASN GLU PRO ASP ILE GLU ASN ILE TRP GLU GLN SEQRES 7 B 446 LEU ARG ASP ARG ILE GLN ASP LEU VAL ASP GLU SER ILE SEQRES 8 B 446 ILE ASP ALA ILE ASN GLY ILE LEU ASP SER LYS ILE LYS SEQRES 9 B 446 GLU THR ARG ASP LYS ILE GLN ASP ILE ASN GLU THR ILE SEQRES 10 B 446 GLU ASN PHE GLY TYR ALA ALA ALA LYS ASP ASP TYR ILE SEQRES 11 B 446 GLY LEU VAL THR HIS TYR LEU ILE GLY LEU GLU GLU ASN SEQRES 12 B 446 PHE LYS ARG GLU LEU ASP GLY ASP GLU TRP LEU GLY TYR SEQRES 13 B 446 ALA ILE LEU PRO LEU LEU ALA THR THR VAL SER LEU GLN SEQRES 14 B 446 ILE THR TYR MET ALA CYS GLY LEU ASP TYR LYS ASP GLU SEQRES 15 B 446 PHE GLY PHE THR ASP SER ASP VAL HIS LYS LEU THR ARG SEQRES 16 B 446 ASN ILE ASP LYS LEU TYR ASP ASP VAL SER SER TYR ILE SEQRES 17 B 446 THR GLU LEU ALA ALA TRP ALA ASP ASN ASP SER TYR ASN SEQRES 18 B 446 ASN ALA ASN GLN ASP ASN VAL TYR ASP GLU VAL MET GLY SEQRES 19 B 446 ALA ARG SER TRP CYS THR VAL HIS GLY PHE GLU HIS MET SEQRES 20 B 446 LEU ILE TRP GLN LYS ILE LYS GLU LEU LYS LYS VAL ASP SEQRES 21 B 446 VAL PHE VAL HIS SER ASN LEU ILE SER TYR SER PRO ALA SEQRES 22 B 446 VAL GLY PHE PRO SER GLY ASN PHE ASN TYR ILE ALA THR SEQRES 23 B 446 GLY THR GLU ASP GLU ILE PRO GLN PRO LEU LYS PRO ASN SEQRES 24 B 446 MET PHE GLY GLU ARG ARG ASN ARG ILE VAL LYS ILE GLU SEQRES 25 B 446 SER TRP ASN SER ILE GLU ILE HIS TYR TYR ASN ARG VAL SEQRES 26 B 446 GLY ARG LEU LYS LEU THR TYR GLU ASN GLY GLU VAL VAL SEQRES 27 B 446 GLU LEU GLY LYS ALA HIS LYS TYR ASP GLU HIS TYR GLN SEQRES 28 B 446 SER ILE GLU LEU ASN GLY ALA TYR ILE LYS TYR VAL ASP SEQRES 29 B 446 VAL ILE ALA ASN GLY PRO GLU ALA ILE ASP ARG ILE VAL SEQRES 30 B 446 PHE HIS PHE SER ASP ASP ARG THR PHE VAL VAL GLY GLU SEQRES 31 B 446 ASN SER GLY LYS PRO SER VAL ARG LEU GLN LEU GLU GLY SEQRES 32 B 446 HIS PHE ILE CYS GLY MET LEU ALA ASP GLN GLU GLY SER SEQRES 33 B 446 ASP LYS VAL ALA ALA PHE SER VAL ALA TYR GLU LEU PHE SEQRES 34 B 446 HIS PRO ASP GLU PHE GLY THR GLU LYS LEU GLU HIS HIS SEQRES 35 B 446 HIS HIS HIS HIS FORMUL 3 HOH *995(H2 O) HELIX 1 1 ASN A 18 LYS A 22 5 5 HELIX 2 2 ASN A 34 GLY A 44 1 11 HELIX 3 3 LEU A 45 ILE A 48 5 4 HELIX 4 4 GLY A 53 TRP A 63 1 11 HELIX 5 5 ASN A 74 GLN A 84 1 11 HELIX 6 6 ASP A 88 SER A 101 1 14 HELIX 7 7 SER A 101 GLY A 121 1 21 HELIX 8 8 GLY A 121 TYR A 136 1 16 HELIX 9 9 GLY A 139 LYS A 145 5 7 HELIX 10 10 GLU A 152 TYR A 179 1 28 HELIX 11 11 TYR A 179 GLY A 184 1 6 HELIX 12 12 THR A 186 ASN A 222 1 37 HELIX 13 13 ASN A 227 GLY A 243 1 17 HELIX 14 14 GLY A 243 LYS A 257 1 15 HELIX 15 15 SER A 278 GLY A 287 1 10 HELIX 16 16 THR A 288 ILE A 292 5 5 HELIX 17 17 HIS A 430 GLY A 435 1 6 HELIX 18 18 ASN B 34 GLY B 44 1 11 HELIX 19 19 LEU B 45 ILE B 48 5 4 HELIX 20 20 GLY B 53 TRP B 63 1 11 HELIX 21 21 ASN B 74 GLN B 84 1 11 HELIX 22 22 ASP B 88 SER B 101 1 14 HELIX 23 23 SER B 101 GLY B 121 1 21 HELIX 24 24 GLY B 121 TYR B 136 1 16 HELIX 25 25 GLY B 139 LYS B 145 5 7 HELIX 26 26 GLU B 152 TYR B 179 1 28 HELIX 27 27 TYR B 179 GLY B 184 1 6 HELIX 28 28 THR B 186 ASN B 222 1 37 HELIX 29 29 ASN B 227 HIS B 242 1 16 HELIX 30 30 GLY B 243 LYS B 257 1 15 HELIX 31 31 SER B 278 GLY B 287 1 10 HELIX 32 32 THR B 288 ILE B 292 5 5 HELIX 33 33 HIS B 430 GLY B 435 1 6 SHEET 1 A 5 TYR A 29 GLU A 30 0 SHEET 2 A 5 VAL A 397 LEU A 401 1 O GLN A 400 N GLU A 30 SHEET 3 A 5 ILE A 360 ASN A 368 -1 N VAL A 363 O LEU A 399 SHEET 4 A 5 ALA A 372 PHE A 380 -1 O VAL A 377 N ASP A 364 SHEET 5 A 5 THR A 385 GLY A 389 -1 O PHE A 386 N PHE A 378 SHEET 1 B 3 ILE A 268 TYR A 270 0 SHEET 2 B 3 ALA A 421 LEU A 428 -1 O TYR A 426 N SER A 269 SHEET 3 B 3 VAL A 274 GLY A 275 -1 N VAL A 274 O PHE A 422 SHEET 1 C 3 ILE A 268 TYR A 270 0 SHEET 2 C 3 ALA A 421 LEU A 428 -1 O TYR A 426 N SER A 269 SHEET 3 C 3 HIS A 404 ASP A 412 -1 N PHE A 405 O GLU A 427 SHEET 1 D 2 MET A 300 PHE A 301 0 SHEET 2 D 2 ARG A 304 ARG A 305 -1 O ARG A 304 N PHE A 301 SHEET 1 E 4 VAL A 337 LEU A 340 0 SHEET 2 E 4 TYR A 322 TYR A 332 -1 N LEU A 328 O LEU A 340 SHEET 3 E 4 ILE A 308 ILE A 319 -1 N VAL A 309 O THR A 331 SHEET 4 E 4 GLU A 348 GLU A 354 -1 O GLU A 348 N ASN A 315 SHEET 1 F 5 TYR B 29 GLU B 30 0 SHEET 2 F 5 SER B 396 LEU B 401 1 O GLN B 400 N GLU B 30 SHEET 3 F 5 ILE B 360 ASN B 368 -1 N VAL B 363 O LEU B 399 SHEET 4 F 5 ALA B 372 PHE B 380 -1 O VAL B 377 N ASP B 364 SHEET 5 F 5 THR B 385 GLY B 389 -1 O PHE B 386 N PHE B 378 SHEET 1 G 3 ILE B 268 TYR B 270 0 SHEET 2 G 3 ALA B 421 LEU B 428 -1 O TYR B 426 N SER B 269 SHEET 3 G 3 VAL B 274 GLY B 275 -1 N VAL B 274 O PHE B 422 SHEET 1 H 3 ILE B 268 TYR B 270 0 SHEET 2 H 3 ALA B 421 LEU B 428 -1 O TYR B 426 N SER B 269 SHEET 3 H 3 HIS B 404 ASP B 412 -1 N PHE B 405 O GLU B 427 SHEET 1 I 2 MET B 300 PHE B 301 0 SHEET 2 I 2 ARG B 304 ARG B 305 -1 O ARG B 304 N PHE B 301 SHEET 1 J 4 VAL B 337 LEU B 340 0 SHEET 2 J 4 VAL B 325 TYR B 332 -1 N LEU B 328 O LEU B 340 SHEET 3 J 4 ILE B 308 ASN B 315 -1 N VAL B 309 O THR B 331 SHEET 4 J 4 GLU B 348 GLU B 354 -1 O GLU B 348 N ASN B 315 CISPEP 1 GLN A 294 PRO A 295 0 6.48 CISPEP 2 GLY A 369 PRO A 370 0 -1.22 CISPEP 3 GLN B 294 PRO B 295 0 12.72 CISPEP 4 GLY B 369 PRO B 370 0 -0.54 CRYST1 120.897 128.618 117.104 90.00 90.00 90.00 C 2 2 21 16 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 0.008272 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008539 0.00000