HEADER PROTEIN BINDING 08-NOV-17 5YQW TITLE STRUCTURE AND FUNCTION OF A NOVEL PERIPLASMIC CHITOOLIGOSACCHARIDE- TITLE 2 BINDING PROTEIN FROM MARINE VIBRIO BACTERIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE ABC TRANSPORTER, PERIPLASMIC PEPTIDE-BINDING COMPND 3 PROTEIN; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: CHITOOLIGOSACCHARIDE-BINDING PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO HARVEYI (STRAIN 1DA3); SOURCE 3 ORGANISM_TAXID: 673519; SOURCE 4 STRAIN: 1DA3; SOURCE 5 GENE: VME_26970; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMI (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET23A KEYWDS CHITOOLIGOSACCHARIDE-BINDING PROTEIN, VIBRIO HARVEYI, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR W.SUGINTA,N.SRITHO,A.RANOK,Y.KITAOKU,D.M.BULMER,B.VAN DEN BERG, AUTHOR 2 T.FUKAMIZO REVDAT 4 22-NOV-23 5YQW 1 HETSYN REVDAT 3 29-JUL-20 5YQW 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 FORMUL LINK SITE ATOM REVDAT 2 18-APR-18 5YQW 1 JRNL REVDAT 1 21-FEB-18 5YQW 0 JRNL AUTH W.SUGINTA,N.SRITHO,A.RANOK,D.M.BULMER,Y.KITAOKU, JRNL AUTH 2 B.VAN DEN BERG,T.FUKAMIZO JRNL TITL STRUCTURE AND FUNCTION OF A NOVEL PERIPLASMIC JRNL TITL 2 CHITOOLIGOSACCHARIDE-BINDING PROTEIN FROM JRNL TITL 3 MARINEVIBRIOBACTERIA. JRNL REF J. BIOL. CHEM. V. 293 5150 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29444825 JRNL DOI 10.1074/JBC.RA117.001012 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.SONGSIRIRITTHIGUL,S.PANTOOM,A.H.AGUDA,R.C.ROBINSON, REMARK 1 AUTH 2 W.SUGINTA REMARK 1 TITL CRYSTAL STRUCTURES OF VIBRIO HARVEYI CHITINASE A COMPLEXED REMARK 1 TITL 2 WITH CHITOOLIGOSACCHARIDES: IMPLICATIONS FOR THE CATALYTIC REMARK 1 TITL 3 MECHANISM. REMARK 1 REF J. STRUCT. BIOL. V. 162 491 2008 REMARK 1 REFN ESSN 1095-8657 REMARK 1 PMID 18467126 REMARK 1 DOI 10.1016/J.JSB.2008.03.008 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 107022 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 5473 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) : 1.36 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7359 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.3800 REMARK 3 BIN FREE R VALUE SET COUNT : 404 REMARK 3 BIN FREE R VALUE : 0.4050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4260 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 461 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.27000 REMARK 3 B22 (A**2) : 0.27000 REMARK 3 B33 (A**2) : -0.86000 REMARK 3 B12 (A**2) : 0.13000 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): 0.064 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.067 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.536 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4505 ; 0.030 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6150 ; 2.209 ; 1.938 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 554 ; 6.673 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 226 ;36.823 ;24.912 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 697 ;13.533 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;16.967 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 658 ; 0.185 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3527 ; 0.016 ; 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): 2160 ; 1.599 ; 1.432 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2708 ; 2.226 ; 2.146 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2345 ; 2.935 ; 1.682 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): 6669 ; 5.376 ;20.736 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: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5YQW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005697. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819 REMARK 200 MONOCHROMATOR : 0.920 REMARK 200 OPTICS : FIXED MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 115984 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 46.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 1.65900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1ZU0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.09M HALOGENS (NAF, NABR, NAI), 0.1M REMARK 280 BUFFER 2 (HEPES/MOPS) PH 7.5, 37.5% MPD_P1K_P3350 MIX, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K 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 102.14733 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 204.29467 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 204.29467 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 102.14733 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 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 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 A1159 LIES ON A SPECIAL POSITION. 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 1039 O HOH A 1056 1.65 REMARK 500 O HOH A 969 O HOH A 1107 1.71 REMARK 500 O HOH A 701 O HOH A 704 1.78 REMARK 500 O HOH A 704 O HOH A 728 1.88 REMARK 500 O HOH A 1084 O HOH A 1132 1.89 REMARK 500 O HOH A 1103 O HOH A 1123 1.91 REMARK 500 O HOH A 718 O HOH A 795 1.92 REMARK 500 O HOH A 701 O HOH A 1064 2.04 REMARK 500 O HOH A 1092 O HOH A 1132 2.05 REMARK 500 O HOH A 929 O HOH A 1138 2.05 REMARK 500 O HOH A 866 O HOH A 951 2.06 REMARK 500 O HOH A 803 O HOH A 986 2.11 REMARK 500 O HOH A 1157 O HOH A 1160 2.12 REMARK 500 O HOH A 1091 O HOH A 1106 2.13 REMARK 500 O LEU A 524 O HOH A 701 2.18 REMARK 500 O HOH A 841 O HOH A 1052 2.18 REMARK 500 O HOH A 1018 O HOH A 1080 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 GLU A 36 CD GLU A 36 OE2 -0.067 REMARK 500 TYR A 185 CG TYR A 185 CD1 0.083 REMARK 500 GLU A 354 CD GLU A 354 OE1 0.073 REMARK 500 TYR A 410 CG TYR A 410 CD1 0.085 REMARK 500 TYR A 455 CG TYR A 455 CD1 0.083 REMARK 500 TYR A 488 CG TYR A 488 CD1 0.082 REMARK 500 TYR A 492 CE1 TYR A 492 CZ 0.112 REMARK 500 TRP A 501 CG TRP A 501 CD1 0.088 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 MET A 59 CG - SD - CE ANGL. DEV. = 13.6 DEGREES REMARK 500 ASP A 62 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 71 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 LYS A 143 CD - CE - NZ ANGL. DEV. = -14.0 DEGREES REMARK 500 ARG A 271 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 279 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 365 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 385 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP A 404 CB - CG - OD1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG A 519 NE - CZ - NH1 ANGL. DEV. = 4.6 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 LEU A 22 62.35 -108.59 REMARK 500 ASP A 32 -59.89 77.74 REMARK 500 ARG A 52 -103.35 -110.58 REMARK 500 LYS A 97 77.49 -119.82 REMARK 500 ASN A 116 -173.91 -170.21 REMARK 500 SER A 220 41.11 -149.78 REMARK 500 THR A 229 -74.14 -102.00 REMARK 500 TYR A 241 74.45 -119.73 REMARK 500 ALA A 244 -155.24 -117.11 REMARK 500 ASN A 323 80.56 -164.18 REMARK 500 ASP A 404 -61.40 -106.40 REMARK 500 MET A 439 42.04 -82.00 REMARK 500 REMARK 500 REMARK: NULL DBREF 5YQW A -1 530 UNP D0XC84 D0XC84_VIBH1 29 560 SEQRES 1 A 532 ALA GLU ARG SER GLU LEU THR ILE HIS PRO LYS GLU PHE SEQRES 2 A 532 THR THR PHE VAL ARG ASN PHE ASN PRO PHE LEU GLY ALA SEQRES 3 A 532 THR ASN LEU HIS THR THR THR ASP PHE ILE TYR GLU PRO SEQRES 4 A 532 LEU VAL VAL PHE ASN GLU MET HIS GLY ASN THR PRO VAL SEQRES 5 A 532 PHE ARG LEU ALA GLU ASN PHE GLN MET SER ASP ASP LEU SEQRES 6 A 532 MET SER VAL THR PHE ASP ILE ARG LYS GLY VAL LYS TRP SEQRES 7 A 532 SER ASP GLY GLU ALA PHE THR ALA ASP ASP VAL VAL TYR SEQRES 8 A 532 SER PHE ASN LEU VAL LYS GLU LYS PRO GLU LEU ASP GLN SEQRES 9 A 532 SER GLY ILE ASN SER TRP VAL THR GLY VAL GLU LYS VAL SEQRES 10 A 532 ASN ASP TYR GLN VAL LYS PHE ARG LEU SER GLU ALA ASN SEQRES 11 A 532 SER ASN VAL PRO TYR GLU ILE ALA LYS VAL PRO VAL VAL SEQRES 12 A 532 PRO LYS HIS VAL TRP SER LYS VAL LYS ASP PRO SER THR SEQRES 13 A 532 PHE THR ASN GLU ASN PRO VAL GLY SER GLY PRO PHE THR SEQRES 14 A 532 VAL ILE ASP THR PHE THR PRO GLN LEU TYR ILE GLN CYS SEQRES 15 A 532 GLU ASN PRO ASN TYR TRP ASP ALA ALA ASN LEU ASP VAL SEQRES 16 A 532 ASP CYS LEU ARG VAL PRO GLN ILE ALA ASN ASN ASP GLN SEQRES 17 A 532 PHE LEU GLY LYS VAL VAL ASN GLY GLU MET ASP TRP THR SEQRES 18 A 532 SER SER PHE VAL PRO ASP ILE ASP ARG THR TYR ALA ALA SEQRES 19 A 532 ALA SER PRO LYS HIS HIS TYR TRP TYR PRO PRO ALA GLY SEQRES 20 A 532 THR GLN ALA PHE VAL VAL ASN PHE LYS ASN PRO ASP ALA SEQRES 21 A 532 ALA LYS ASN GLU ALA LEU THR ASN VAL ASP PHE ARG ARG SEQRES 22 A 532 ALA PHE SER MET ALA LEU ASP ARG GLN THR ILE ILE ASP SEQRES 23 A 532 ILE ALA PHE TYR GLY GLY GLY THR VAL ASN ASP PHE ALA SEQRES 24 A 532 SER GLY LEU GLY TYR ALA PHE GLU ALA TRP SER ASP GLU SEQRES 25 A 532 LYS THR HIS ASP LYS PHE LYS ALA TYR ASN SER TYR ASN SEQRES 26 A 532 ALA GLU GLY ALA LYS LYS LEU LEU ALA LYS ALA GLY PHE SEQRES 27 A 532 LYS ASP VAL ASN LYS ASP GLY PHE VAL ASP THR PRO SER SEQRES 28 A 532 GLY LYS SER PHE GLU LEU LEU ILE GLN SER PRO ASN GLY SEQRES 29 A 532 TRP THR ASP PHE ASN ASN THR VAL GLN LEU ALA VAL GLU SEQRES 30 A 532 GLN LEU ALA GLU VAL GLY ILE LYS ALA ARG ALA ARG THR SEQRES 31 A 532 PRO ASP PHE SER VAL TYR ASN GLN ALA MET LEU GLU GLY SEQRES 32 A 532 THR TYR ASP VAL ALA TYR THR ASN TYR PHE HIS GLY ALA SEQRES 33 A 532 ASP PRO TYR THR TYR TRP ASN SER ALA TYR ASN SER ALA SEQRES 34 A 532 LEU GLN SER GLY ASP GLY MET PRO ARG PHE ALA MET HIS SEQRES 35 A 532 PHE TYR LYS ASN GLU LYS LEU ASP GLY LEU LEU ASN SER SEQRES 36 A 532 PHE TYR LYS THR ALA ASP LYS GLN GLU GLN LEU GLU ILE SEQRES 37 A 532 ALA HIS GLY ILE GLN GLN ILE ILE ALA GLN ASP GLN VAL SEQRES 38 A 532 THR ILE PRO VAL LEU SER GLY ALA TYR MET TYR GLN TYR SEQRES 39 A 532 ASN THR THR ARG PHE THR GLY TRP TRP ASN GLU GLU ASN SEQRES 40 A 532 PRO LYS GLY ARG PRO ASN ILE TRP ALA GLY ILE PRO GLU SEQRES 41 A 532 ARG LEU LEU HIS VAL LEU ASP LEU LYS PRO VAL LYS HET NAG B 1 15 HET NAG B 2 14 HET P4G A 601 11 HET P4G A 602 11 HET NI A 603 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE HETNAM NI NICKEL (II) ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 3 P4G 2(C8 H18 O3) FORMUL 5 NI NI 2+ FORMUL 6 HOH *461(H2 O) HELIX 1 AA1 GLU A 43 GLY A 46 5 4 HELIX 2 AA2 THR A 83 LYS A 97 1 15 HELIX 3 AA3 PRO A 98 ASP A 101 5 4 HELIX 4 AA4 GLY A 104 TRP A 108 1 5 HELIX 5 AA5 ASN A 130 LYS A 137 1 8 HELIX 6 AA6 PRO A 142 SER A 147 1 6 HELIX 7 AA7 ASP A 187 LEU A 191 5 5 HELIX 8 AA8 ASN A 203 ASN A 213 1 11 HELIX 9 AA9 THR A 229 SER A 234 1 6 HELIX 10 AB1 ASP A 257 THR A 265 1 9 HELIX 11 AB2 ASN A 266 LEU A 277 1 12 HELIX 12 AB3 ASP A 278 PHE A 287 1 10 HELIX 13 AB4 GLY A 301 SER A 308 5 8 HELIX 14 AB5 ASP A 309 LYS A 317 1 9 HELIX 15 AB6 ALA A 318 SER A 321 5 4 HELIX 16 AB7 ASN A 323 GLY A 335 1 13 HELIX 17 AB8 TRP A 363 VAL A 380 1 18 HELIX 18 AB9 ASP A 390 GLU A 400 1 11 HELIX 19 AC1 PRO A 416 ASN A 425 1 10 HELIX 20 AC2 SER A 426 GLN A 429 5 4 HELIX 21 AC3 ASN A 444 PHE A 454 1 11 HELIX 22 AC4 ASP A 459 GLN A 478 1 20 HELIX 23 AC5 PRO A 517 LEU A 524 1 8 SHEET 1 AA1 4 GLU A 3 THR A 5 0 SHEET 2 AA1 4 CYS A 195 PRO A 199 1 O CYS A 195 N LEU A 4 SHEET 3 AA1 4 LEU A 176 GLU A 181 -1 N GLN A 179 O LEU A 196 SHEET 4 AA1 4 PHE A 166 THR A 173 -1 N VAL A 168 O CYS A 180 SHEET 1 AA2 2 VAL A 39 PHE A 41 0 SHEET 2 AA2 2 PRO A 49 PHE A 51 -1 O VAL A 50 N VAL A 40 SHEET 1 AA3 4 ALA A 54 MET A 59 0 SHEET 2 AA3 4 SER A 65 ILE A 70 -1 O ASP A 69 N ASN A 56 SHEET 3 AA3 4 GLN A 119 LEU A 124 -1 O PHE A 122 N VAL A 66 SHEET 4 AA3 4 VAL A 109 ASN A 116 -1 N GLU A 113 O LYS A 121 SHEET 1 AA4 3 TRP A 218 THR A 219 0 SHEET 2 AA4 3 GLN A 491 ASN A 493 -1 O GLN A 491 N THR A 219 SHEET 3 AA4 3 HIS A 237 TYR A 239 -1 N HIS A 238 O TYR A 492 SHEET 1 AA5 6 THR A 292 VAL A 293 0 SHEET 2 AA5 6 ILE A 481 ALA A 487 -1 O SER A 485 N THR A 292 SHEET 3 AA5 6 PRO A 243 VAL A 251 -1 N PHE A 249 O ILE A 481 SHEET 4 AA5 6 VAL A 405 ASN A 409 -1 O ALA A 406 N VAL A 250 SHEET 5 AA5 6 LEU A 355 GLN A 358 1 N GLN A 358 O VAL A 405 SHEET 6 AA5 6 ALA A 384 ARG A 387 1 O ARG A 385 N ILE A 357 SHEET 1 AA6 2 PHE A 497 THR A 498 0 SHEET 2 AA6 2 LYS A 527 PRO A 528 -1 O LYS A 527 N THR A 498 SSBOND 1 CYS A 180 CYS A 195 1555 1555 2.14 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 CRYST1 54.730 54.730 306.442 90.00 90.00 120.00 P 31 2 1 6 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 0.018271 0.010549 0.000000 0.00000 SCALE2 0.000000 0.021098 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003263 0.00000