HEADER TRANSCRIPTION REGULATOR 23-JAN-13 4IVN TITLE THE VIBRIO VULNIFICUS NANR PROTEIN COMPLEXED WITH MANNAC-6P COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NANR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 3 ORGANISM_TAXID: 196600; SOURCE 4 STRAIN: YJ016; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOMERASE FOLD, NAN OPERON REGULATOR FOR SIALIC ACID CATABOLISM, KEYWDS 2 TRANSCRIPTION REGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR J.HWANG,M.H.KIM REVDAT 4 20-MAR-24 4IVN 1 HETSYN REVDAT 3 29-JUL-20 4IVN 1 COMPND REMARK HETNAM SITE REVDAT 2 20-NOV-13 4IVN 1 JRNL REVDAT 1 17-JUL-13 4IVN 0 JRNL AUTH J.HWANG,B.S.KIM,S.Y.JANG,J.G.LIM,D.J.YOU,H.S.JUNG,T.K.OH, JRNL AUTH 2 J.O.LEE,S.H.CHOI,M.H.KIM JRNL TITL STRUCTURAL INSIGHTS INTO THE REGULATION OF SIALIC ACID JRNL TITL 2 CATABOLISM BY THE VIBRIO VULNIFICUS TRANSCRIPTIONAL JRNL TITL 3 REPRESSOR NANR JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 E2829 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23832782 JRNL DOI 10.1073/PNAS.1302859110 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 42737 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2268 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2947 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 162 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4004 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 221 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.27000 REMARK 3 B22 (A**2) : -2.27000 REMARK 3 B33 (A**2) : 3.41000 REMARK 3 B12 (A**2) : -1.14000 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): 0.142 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.144 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.106 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.038 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4096 ; 0.021 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5548 ; 2.126 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 521 ; 6.387 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 165 ;35.450 ;23.576 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 716 ;16.845 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;18.969 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 669 ; 0.148 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2984 ; 0.010 ; 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): 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 6 277 B 6 277 366 0.15 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 81 REMARK 3 ORIGIN FOR THE GROUP (A): 17.7780 -5.8420 8.8420 REMARK 3 T TENSOR REMARK 3 T11: 0.0449 T22: 0.1497 REMARK 3 T33: 0.1331 T12: 0.0044 REMARK 3 T13: -0.0544 T23: -0.0500 REMARK 3 L TENSOR REMARK 3 L11: 3.4953 L22: 2.2054 REMARK 3 L33: 2.1117 L12: -0.5910 REMARK 3 L13: 0.7559 L23: 0.5527 REMARK 3 S TENSOR REMARK 3 S11: 0.2213 S12: 0.2193 S13: -0.1430 REMARK 3 S21: -0.1435 S22: -0.2725 S23: 0.3625 REMARK 3 S31: 0.1735 S32: -0.1381 S33: 0.0512 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 91 A 278 REMARK 3 ORIGIN FOR THE GROUP (A): 45.2910 8.9760 13.2780 REMARK 3 T TENSOR REMARK 3 T11: 0.0570 T22: 0.0852 REMARK 3 T33: 0.0778 T12: 0.0414 REMARK 3 T13: 0.0370 T23: 0.0537 REMARK 3 L TENSOR REMARK 3 L11: 0.6889 L22: 0.6680 REMARK 3 L33: 0.8170 L12: -0.0380 REMARK 3 L13: 0.1453 L23: 0.1381 REMARK 3 S TENSOR REMARK 3 S11: 0.0958 S12: 0.1733 S13: 0.0946 REMARK 3 S21: -0.1548 S22: -0.0145 S23: -0.0391 REMARK 3 S31: -0.0769 S32: -0.1389 S33: -0.0812 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 6 B 80 REMARK 3 ORIGIN FOR THE GROUP (A): 82.6480 3.2410 8.3210 REMARK 3 T TENSOR REMARK 3 T11: 0.0362 T22: 0.1890 REMARK 3 T33: 0.2221 T12: 0.0038 REMARK 3 T13: 0.0694 T23: -0.0873 REMARK 3 L TENSOR REMARK 3 L11: 1.7284 L22: 1.3274 REMARK 3 L33: 2.4459 L12: 0.2465 REMARK 3 L13: -1.0201 L23: 0.0720 REMARK 3 S TENSOR REMARK 3 S11: 0.0630 S12: 0.0848 S13: -0.0810 REMARK 3 S21: -0.1023 S22: 0.0872 S23: -0.1534 REMARK 3 S31: -0.0463 S32: 0.4472 S33: -0.1502 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 92 B 277 REMARK 3 ORIGIN FOR THE GROUP (A): 55.3100 -10.8280 14.5630 REMARK 3 T TENSOR REMARK 3 T11: 0.0555 T22: 0.0233 REMARK 3 T33: 0.1270 T12: 0.0218 REMARK 3 T13: -0.0027 T23: -0.0342 REMARK 3 L TENSOR REMARK 3 L11: 0.9177 L22: 0.6147 REMARK 3 L33: 0.8648 L12: -0.0846 REMARK 3 L13: -0.0381 L23: 0.0605 REMARK 3 S TENSOR REMARK 3 S11: 0.1126 S12: 0.1400 S13: -0.1727 REMARK 3 S21: -0.1213 S22: -0.0199 S23: -0.1418 REMARK 3 S31: 0.1198 S32: 0.0177 S33: -0.0927 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: NULL REMARK 4 REMARK 4 4IVN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000077266. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100.15 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45033 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 2000 MME, 0.1M AMMONIUM REMARK 280 SULFATE, 0.3M SODIUM FORMATE, 3% PGA-LM, 0.1M SODIUM ACETATE, PH REMARK 280 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.49067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.98133 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 54.98133 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.49067 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 GLY A 2 REMARK 465 SER A 3 REMARK 465 PRO A 4 REMARK 465 LYS A 5 REMARK 465 GLU A 82 REMARK 465 SER A 83 REMARK 465 ARG A 84 REMARK 465 GLN A 85 REMARK 465 GLN A 86 REMARK 465 ASN A 87 REMARK 465 HIS A 88 REMARK 465 ILE A 89 REMARK 465 GLU A 90 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 SER B 3 REMARK 465 PRO B 4 REMARK 465 LYS B 5 REMARK 465 THR B 81 REMARK 465 GLU B 82 REMARK 465 SER B 83 REMARK 465 ARG B 84 REMARK 465 GLN B 85 REMARK 465 GLN B 86 REMARK 465 ASN B 87 REMARK 465 HIS B 88 REMARK 465 ILE B 89 REMARK 465 GLU B 90 REMARK 465 GLY B 91 REMARK 465 ASN B 278 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 1189 O HOH A 1200 2.18 REMARK 500 O HOH B 1186 O HOH B 1205 2.19 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 HIS A 34 CG HIS A 34 CD2 0.064 REMARK 500 GLU A 160 C GLU A 160 O 0.118 REMARK 500 HIS A 192 CG HIS A 192 CD2 0.055 REMARK 500 THR B 220 CB THR B 220 CG2 -0.202 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 ASP A 161 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 171 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 171 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 227 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 248 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG B 227 NE - CZ - NH2 ANGL. DEV. = -4.0 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 ARG A 227 81.53 63.17 REMARK 500 PRO A 259 -19.64 -49.20 REMARK 500 THR B 50 -143.74 -118.57 REMARK 500 ASP B 201 31.72 70.03 REMARK 500 ARG B 227 76.48 65.91 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 ALA A 277 ASN A 278 -135.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 4IVN A 1 278 UNP Q7MD38 Q7MD38_VIBVY 1 278 DBREF 4IVN B 1 278 UNP Q7MD38 Q7MD38_VIBVY 1 278 SEQRES 1 A 278 MET GLY SER PRO LYS ASN LEU LEU VAL ARG LEU ARG SER SEQRES 2 A 278 ASN MET GLU PRO PHE SER LYS LYS LEU ARG VAL VAL ALA SEQRES 3 A 278 ASP TYR ILE LEU GLU ASN ALA HIS ASP VAL GLN PHE GLN SEQRES 4 A 278 THR ILE THR ASP LEU ALA ARG ASN THR GLN THR SER GLU SEQRES 5 A 278 ALA THR VAL VAL ARG LEU CYS ARG ASP MET GLY TYR LYS SEQRES 6 A 278 GLY TYR SER ASP PHE ARG MET ALA LEU ALA VAL ASP LEU SEQRES 7 A 278 SER GLN THR GLU SER ARG GLN GLN ASN HIS ILE GLU GLY SEQRES 8 A 278 ASP ILE CYS ASP VAL SER ALA GLN SER ALA VAL ASP SER SEQRES 9 A 278 LEU GLN ASP THR ALA LYS LEU ILE ASP ARG LYS SER LEU SEQRES 10 A 278 ALA ARG ILE VAL GLU ARG VAL HIS GLN ALA GLU PHE ILE SEQRES 11 A 278 GLY CYS ILE GLY VAL GLY ALA SER SER ILE VAL GLY ARG SEQRES 12 A 278 TYR LEU ALA TYR ARG LEU ILE ARG ILE GLY LYS LYS ALA SEQRES 13 A 278 ILE MET PHE GLU ASP THR HIS LEU ALA ALA MET SER ALA SEQRES 14 A 278 SER ARG SER SER GLN GLY ASP LEU TRP PHE ALA VAL SER SEQRES 15 A 278 SER SER GLY SER THR LYS GLU VAL ILE HIS ALA ALA GLY SEQRES 16 A 278 LEU ALA TYR LYS ARG ASP ILE PRO VAL VAL SER LEU THR SEQRES 17 A 278 ASN ILE ASN HIS SER PRO LEU SER SER LEU SER THR GLU SEQRES 18 A 278 MET LEU VAL ALA ALA ARG PRO GLU GLY PRO LEU THR GLY SEQRES 19 A 278 GLY ALA PHE ALA SER LYS VAL GLY ALA LEU LEU LEU VAL SEQRES 20 A 278 ASP VAL LEU VAL ASN SER LEU LEU GLU SER TYR PRO GLU SEQRES 21 A 278 TYR LYS ASP SER VAL GLN GLU THR ALA GLU VAL VAL ILE SEQRES 22 A 278 PRO LEU MET ALA ASN SEQRES 1 B 278 MET GLY SER PRO LYS ASN LEU LEU VAL ARG LEU ARG SER SEQRES 2 B 278 ASN MET GLU PRO PHE SER LYS LYS LEU ARG VAL VAL ALA SEQRES 3 B 278 ASP TYR ILE LEU GLU ASN ALA HIS ASP VAL GLN PHE GLN SEQRES 4 B 278 THR ILE THR ASP LEU ALA ARG ASN THR GLN THR SER GLU SEQRES 5 B 278 ALA THR VAL VAL ARG LEU CYS ARG ASP MET GLY TYR LYS SEQRES 6 B 278 GLY TYR SER ASP PHE ARG MET ALA LEU ALA VAL ASP LEU SEQRES 7 B 278 SER GLN THR GLU SER ARG GLN GLN ASN HIS ILE GLU GLY SEQRES 8 B 278 ASP ILE CYS ASP VAL SER ALA GLN SER ALA VAL ASP SER SEQRES 9 B 278 LEU GLN ASP THR ALA LYS LEU ILE ASP ARG LYS SER LEU SEQRES 10 B 278 ALA ARG ILE VAL GLU ARG VAL HIS GLN ALA GLU PHE ILE SEQRES 11 B 278 GLY CYS ILE GLY VAL GLY ALA SER SER ILE VAL GLY ARG SEQRES 12 B 278 TYR LEU ALA TYR ARG LEU ILE ARG ILE GLY LYS LYS ALA SEQRES 13 B 278 ILE MET PHE GLU ASP THR HIS LEU ALA ALA MET SER ALA SEQRES 14 B 278 SER ARG SER SER GLN GLY ASP LEU TRP PHE ALA VAL SER SEQRES 15 B 278 SER SER GLY SER THR LYS GLU VAL ILE HIS ALA ALA GLY SEQRES 16 B 278 LEU ALA TYR LYS ARG ASP ILE PRO VAL VAL SER LEU THR SEQRES 17 B 278 ASN ILE ASN HIS SER PRO LEU SER SER LEU SER THR GLU SEQRES 18 B 278 MET LEU VAL ALA ALA ARG PRO GLU GLY PRO LEU THR GLY SEQRES 19 B 278 GLY ALA PHE ALA SER LYS VAL GLY ALA LEU LEU LEU VAL SEQRES 20 B 278 ASP VAL LEU VAL ASN SER LEU LEU GLU SER TYR PRO GLU SEQRES 21 B 278 TYR LYS ASP SER VAL GLN GLU THR ALA GLU VAL VAL ILE SEQRES 22 B 278 PRO LEU MET ALA ASN HET BMX A1000 19 HET BMX B1000 19 HETNAM BMX 2-ACETAMIDO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE HETSYN BMX 2-(ACETYLAMINO)-2-DEOXY-6-O-PHOSPHONO-ALPHA-D- HETSYN 2 BMX MANNOPYRANOSE; N-ACETYL-6-O-PHOSPHONO-ALPHA-D- HETSYN 3 BMX MANNOSAMINE; 2-ACETAMIDO-2-DEOXY-6-O-PHOSPHONO-ALPHA- HETSYN 4 BMX D-MANNOSE; 2-ACETAMIDO-2-DEOXY-6-O-PHOSPHONO-D- HETSYN 5 BMX MANNOSE; 2-ACETAMIDO-2-DEOXY-6-O-PHOSPHONO-MANNOSE FORMUL 3 BMX 2(C8 H16 N O9 P) FORMUL 5 HOH *221(H2 O) HELIX 1 1 ASN A 6 ASN A 14 1 9 HELIX 2 2 SER A 19 GLN A 37 1 19 HELIX 3 3 THR A 40 GLN A 49 1 10 HELIX 4 4 SER A 51 MET A 62 1 12 HELIX 5 5 GLY A 66 SER A 79 1 14 HELIX 6 6 ASP A 92 ILE A 112 1 21 HELIX 7 7 ASP A 113 ALA A 127 1 15 HELIX 8 8 GLY A 136 ILE A 152 1 17 HELIX 9 9 ASP A 161 ARG A 171 1 11 HELIX 10 10 THR A 187 ARG A 200 1 14 HELIX 11 11 LEU A 215 SER A 219 5 5 HELIX 12 12 ALA A 236 TYR A 258 1 23 HELIX 13 13 GLU A 260 VAL A 271 1 12 HELIX 14 14 VAL A 272 MET A 276 5 5 HELIX 15 15 LEU B 7 ASN B 14 1 8 HELIX 16 16 SER B 19 GLN B 37 1 19 HELIX 17 17 THR B 40 GLN B 49 1 10 HELIX 18 18 SER B 51 MET B 62 1 12 HELIX 19 19 GLY B 66 GLN B 80 1 15 HELIX 20 20 ILE B 93 ILE B 112 1 20 HELIX 21 21 ASP B 113 ALA B 127 1 15 HELIX 22 22 GLY B 136 ILE B 152 1 17 HELIX 23 23 ASP B 161 ARG B 171 1 11 HELIX 24 24 THR B 187 ARG B 200 1 14 HELIX 25 25 SER B 213 SER B 219 5 7 HELIX 26 26 ALA B 236 TYR B 258 1 23 HELIX 27 27 GLU B 260 VAL B 271 1 12 HELIX 28 28 VAL B 272 MET B 276 5 5 SHEET 1 A 5 ALA A 156 PHE A 159 0 SHEET 2 A 5 PHE A 129 ILE A 133 1 N CYS A 132 O ILE A 157 SHEET 3 A 5 ASP A 176 VAL A 181 1 O VAL A 181 N ILE A 133 SHEET 4 A 5 VAL A 204 THR A 208 1 O VAL A 205 N TRP A 178 SHEET 5 A 5 GLU A 221 VAL A 224 1 O LEU A 223 N SER A 206 SHEET 1 B 5 LYS B 155 PHE B 159 0 SHEET 2 B 5 PHE B 129 ILE B 133 1 N CYS B 132 O PHE B 159 SHEET 3 B 5 ASP B 176 VAL B 181 1 O VAL B 181 N ILE B 133 SHEET 4 B 5 VAL B 204 THR B 208 1 O VAL B 205 N TRP B 178 SHEET 5 B 5 GLU B 221 VAL B 224 1 O LEU B 223 N SER B 206 CRYST1 109.205 109.205 82.472 90.00 90.00 120.00 P 31 2 1 12 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 0.009157 0.005287 0.000000 0.00000 SCALE2 0.000000 0.010574 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012125 0.00000