HEADER HYDROLASE 04-FEB-08 2VNG TITLE FAMILY 51 CARBOHYDRATE BINDING MODULE FROM A FAMILY 98 GLYCOSIDE TITLE 2 HYDROLASE PRODUCED BY CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH BLOOD TITLE 3 GROUP A-TRISACCHARIDE LIGAND. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CPE0329; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CARBOHYDRATE-BINDING MODULE FAMILY 51, RESIDUES 27-206; COMPND 5 SYNONYM: GLYCOSIDE HYDROLASE FAMILY 98; COMPND 6 EC: 3.2.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS; SOURCE 3 ORGANISM_TAXID: 1502; SOURCE 4 ATCC: 13124; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 STAR; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS FAMILY 51 CARBOHYDRATE BINDING MODULE, CLOSTRIDIUM PERFRINGENS, KEYWDS 2 FAMILY 98 GLYCOSIDE HYDROLASE, A-TRISACCHARIDE, BLOOD GROUP ANTIGEN, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.J.GREGG,R.FINN,D.W.ABBOTT,A.B.BORASTON REVDAT 7 08-MAY-24 2VNG 1 HETSYN REVDAT 6 29-JUL-20 2VNG 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 05-JUL-17 2VNG 1 REMARK REVDAT 4 24-FEB-09 2VNG 1 VERSN REVDAT 3 06-MAY-08 2VNG 1 JRNL REMARK REVDAT 2 04-MAR-08 2VNG 1 AUTHOR JRNL REVDAT 1 19-FEB-08 2VNG 0 JRNL AUTH K.J.GREGG,R.FINN,D.W.ABBOTT,A.B.BORASTON JRNL TITL DIVERGENT MODES OF GLYCAN RECOGNITION BY A NEW FAMILY OF JRNL TITL 2 CARBOHYDRATE-BINDING MODULES JRNL REF J.BIOL.CHEM. V. 283 12604 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18292090 JRNL DOI 10.1074/JBC.M709865200 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 57807 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3079 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.43 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3264 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.5310 REMARK 3 BIN FREE R VALUE SET COUNT : 160 REMARK 3 BIN FREE R VALUE : 0.7770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2652 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 585 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.83000 REMARK 3 B22 (A**2) : 0.11000 REMARK 3 B33 (A**2) : -0.93000 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): 0.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.133 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2829 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1889 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3852 ; 1.881 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4629 ; 0.978 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 364 ; 7.142 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;38.101 ;25.763 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 463 ;11.687 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;22.875 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 450 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3119 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 533 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 548 ; 0.259 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2019 ; 0.202 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1405 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1486 ; 0.094 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 478 ; 0.166 ; 0.200 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): 26 ; 0.371 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 57 ; 0.358 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 50 ; 0.244 ; 0.200 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): 1783 ; 2.256 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2817 ; 2.913 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1199 ; 4.018 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1024 ; 4.926 ; 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): 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 : 1.40 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 2VNG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1290035151. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-002 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : OSMIC BLUE REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57807 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 56.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 200 DATA REDUNDANCY : 3.410 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.8 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 34.84150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.37700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.84150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.37700 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 A2274 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2275 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2045 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 GLU A 32 REMARK 465 VAL A 33 REMARK 465 TYR A 34 REMARK 465 ALA A 35 REMARK 465 LEU A 36 REMARK 465 GLU A 37 REMARK 465 GLU A 38 REMARK 465 VAL A 210 REMARK 465 ASN A 211 REMARK 465 GLU B 32 REMARK 465 VAL B 33 REMARK 465 TYR B 34 REMARK 465 ALA B 35 REMARK 465 LEU B 36 REMARK 465 GLU B 37 REMARK 465 ASN B 211 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 40 CD REMARK 470 GLN A 134 CG CD NE2 REMARK 470 GLU A 176 CG CD REMARK 470 LYS A 179 CE NZ REMARK 470 GLU A 189 CD OE1 REMARK 470 GLU B 85 CG CD REMARK 470 GLU B 133 CG REMARK 470 LYS B 148 CE NZ REMARK 470 GLU B 189 CD OE1 OE2 REMARK 470 LYS B 190 CD CE 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 B 2082 O HOH B 2150 2.16 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 OE2 GLU A 85 ND2 ASN B 129 4456 1.90 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 TYR A 121 CD1 TYR A 121 CE1 0.094 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 B 40 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 40 NE - CZ - NH2 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 SER A 102 51.09 -119.29 REMARK 500 GLN B 134 -18.82 -49.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2084 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH B2046 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH B2047 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH B2079 DISTANCE = 6.81 ANGSTROMS REMARK 525 HOH B2147 DISTANCE = 6.60 ANGSTROMS REMARK 525 HOH B2197 DISTANCE = 6.70 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1213 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 137 O REMARK 620 2 ALA A 187 O 85.2 REMARK 620 3 LYS A 190 O 166.5 81.3 REMARK 620 4 ASP A 194 OD1 76.2 135.0 114.0 REMARK 620 5 ASP A 194 OD2 94.7 90.7 85.7 51.5 REMARK 620 6 HOH A2196 O 105.0 159.9 87.9 64.9 105.4 REMARK 620 7 HOH A2276 O 92.4 78.8 84.7 141.4 166.8 83.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1214 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 137 O REMARK 620 2 ALA B 187 O 85.8 REMARK 620 3 LYS B 190 O 174.7 95.1 REMARK 620 4 ASP B 194 OD1 76.5 135.1 106.3 REMARK 620 5 ASP B 194 OD2 95.5 92.4 89.6 50.0 REMARK 620 6 HOH B2179 O 104.0 159.3 73.6 65.5 104.6 REMARK 620 7 HOH B2257 O 91.9 79.4 83.1 141.0 168.4 82.1 REMARK 620 N 1 2 3 4 5 6 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. DBREF 2VNG A 32 211 UNP Q8XNK4 Q8XNK4_CLOPE 27 206 DBREF 2VNG B 32 211 UNP Q8XNK4 Q8XNK4_CLOPE 27 206 SEQRES 1 A 180 GLU VAL TYR ALA LEU GLU GLU SER ARG ASP VAL TYR LEU SEQRES 2 A 180 SER ASP LEU ASP TRP LEU ASN ALA THR HIS GLY ASP ASP SEQRES 3 A 180 THR LYS SER LYS ILE VAL GLN LYS ASN HIS PRO PHE THR SEQRES 4 A 180 PRO GLY ASN ASN ASN GLN SER THR LYS ILE SER LEU LYS SEQRES 5 A 180 MET GLU ASP GLY SER ILE SER GLU PHE GLU LYS GLY LEU SEQRES 6 A 180 GLY THR ILE ALA GLY SER PRO SER THR ILE THR TYR ASP SEQRES 7 A 180 ILE SER GLY ALA GLY VAL THR LYS PHE PHE SER TYR LEU SEQRES 8 A 180 GLY ILE ASP ARG SER ALA ASN PRO ILE ASN GLU GLN TYR SEQRES 9 A 180 ALA LYS VAL ASP LYS ILE GLU VAL VAL VAL ASP GLY LYS SEQRES 10 A 180 VAL ILE TYR SER THR ILE ASN GLN PHE PRO ASN GLY LEU SEQRES 11 A 180 THR TYR GLU THR PRO ALA ILE LYS VAL ASP LEU ASN ILE SEQRES 12 A 180 PRO GLU ASN ALA LYS ARG LEU GLN LEU LYS SER TYR ALA SEQRES 13 A 180 GLY GLU LYS THR TRP GLY ASP GLU VAL VAL TYR ALA ASP SEQRES 14 A 180 ALA LYS PHE THR ALA LYS GLY ASP PHE VAL ASN SEQRES 1 B 180 GLU VAL TYR ALA LEU GLU GLU SER ARG ASP VAL TYR LEU SEQRES 2 B 180 SER ASP LEU ASP TRP LEU ASN ALA THR HIS GLY ASP ASP SEQRES 3 B 180 THR LYS SER LYS ILE VAL GLN LYS ASN HIS PRO PHE THR SEQRES 4 B 180 PRO GLY ASN ASN ASN GLN SER THR LYS ILE SER LEU LYS SEQRES 5 B 180 MET GLU ASP GLY SER ILE SER GLU PHE GLU LYS GLY LEU SEQRES 6 B 180 GLY THR ILE ALA GLY SER PRO SER THR ILE THR TYR ASP SEQRES 7 B 180 ILE SER GLY ALA GLY VAL THR LYS PHE PHE SER TYR LEU SEQRES 8 B 180 GLY ILE ASP ARG SER ALA ASN PRO ILE ASN GLU GLN TYR SEQRES 9 B 180 ALA LYS VAL ASP LYS ILE GLU VAL VAL VAL ASP GLY LYS SEQRES 10 B 180 VAL ILE TYR SER THR ILE ASN GLN PHE PRO ASN GLY LEU SEQRES 11 B 180 THR TYR GLU THR PRO ALA ILE LYS VAL ASP LEU ASN ILE SEQRES 12 B 180 PRO GLU ASN ALA LYS ARG LEU GLN LEU LYS SER TYR ALA SEQRES 13 B 180 GLY GLU LYS THR TRP GLY ASP GLU VAL VAL TYR ALA ASP SEQRES 14 B 180 ALA LYS PHE THR ALA LYS GLY ASP PHE VAL ASN HET GAL C 1 12 HET FUC C 2 10 HET A2G C 3 14 HET GAL D 1 12 HET FUC D 2 10 HET A2G D 3 14 HET CA A1213 1 HET CA B1214 1 HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETNAM CA CALCIUM ION HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN A2G N-ACETYL-ALPHA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 A2G ALPHA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 A2G ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-2-DEOXY-2-AMINO- HETSYN 4 A2G GALACTOSE FORMUL 3 GAL 2(C6 H12 O6) FORMUL 3 FUC 2(C6 H12 O5) FORMUL 3 A2G 2(C8 H15 N O6) FORMUL 5 CA 2(CA 2+) FORMUL 7 HOH *585(H2 O) HELIX 1 1 SER A 45 LEU A 47 5 3 HELIX 2 2 PRO A 68 ASN A 74 1 7 HELIX 3 3 SER B 45 LEU B 47 5 3 HELIX 4 4 PRO B 68 ASN B 74 1 7 SHEET 1 AA 4 ARG A 40 TYR A 43 0 SHEET 2 AA 4 GLU A 195 ALA A 205 -1 O PHE A 203 N VAL A 42 SHEET 3 AA 4 GLY A 95 ILE A 99 -1 O LEU A 96 N TYR A 198 SHEET 4 AA 4 GLN A 64 LYS A 65 -1 O GLN A 64 N GLY A 97 SHEET 1 AB 4 ARG A 40 TYR A 43 0 SHEET 2 AB 4 GLU A 195 ALA A 205 -1 O PHE A 203 N VAL A 42 SHEET 3 AB 4 VAL A 115 ILE A 124 -1 N THR A 116 O THR A 204 SHEET 4 AB 4 ILE A 168 ASN A 173 -1 O ILE A 168 N LEU A 122 SHEET 1 AC 5 ASN A 51 ALA A 52 0 SHEET 2 AC 5 SER A 104 ASP A 109 -1 N THR A 107 O ASN A 51 SHEET 3 AC 5 ARG A 180 TYR A 186 -1 O LEU A 181 N TYR A 108 SHEET 4 AC 5 LYS A 140 VAL A 145 -1 O LYS A 140 N TYR A 186 SHEET 5 AC 5 LYS A 148 SER A 152 -1 O LYS A 148 N VAL A 145 SHEET 1 AD 2 ILE A 80 LYS A 83 0 SHEET 2 AD 2 ILE A 89 PHE A 92 -1 O SER A 90 N LEU A 82 SHEET 1 AE 2 LYS A 137 VAL A 138 0 SHEET 2 AE 2 LEU A 161 THR A 162 -1 O LEU A 161 N VAL A 138 SHEET 1 BA 4 ARG B 40 TYR B 43 0 SHEET 2 BA 4 GLU B 195 ALA B 205 -1 O PHE B 203 N VAL B 42 SHEET 3 BA 4 GLY B 95 ILE B 99 -1 O LEU B 96 N TYR B 198 SHEET 4 BA 4 GLN B 64 LYS B 65 -1 O GLN B 64 N GLY B 97 SHEET 1 BB 4 ARG B 40 TYR B 43 0 SHEET 2 BB 4 GLU B 195 ALA B 205 -1 O PHE B 203 N VAL B 42 SHEET 3 BB 4 VAL B 115 ILE B 124 -1 N THR B 116 O THR B 204 SHEET 4 BB 4 ILE B 168 ASN B 173 -1 O ILE B 168 N LEU B 122 SHEET 1 BC 5 ASN B 51 ALA B 52 0 SHEET 2 BC 5 SER B 104 ASP B 109 -1 N THR B 107 O ASN B 51 SHEET 3 BC 5 ARG B 180 TYR B 186 -1 O LEU B 181 N TYR B 108 SHEET 4 BC 5 LYS B 140 VAL B 145 -1 O LYS B 140 N TYR B 186 SHEET 5 BC 5 LYS B 148 SER B 152 -1 O LYS B 148 N VAL B 145 SHEET 1 BD 2 ILE B 80 LYS B 83 0 SHEET 2 BD 2 ILE B 89 PHE B 92 -1 O SER B 90 N LEU B 82 SHEET 1 BE 2 LYS B 137 VAL B 138 0 SHEET 2 BE 2 LEU B 161 THR B 162 -1 O LEU B 161 N VAL B 138 LINK O2 GAL C 1 C1 FUC C 2 1555 1555 1.45 LINK O3 GAL C 1 C1 A2G C 3 1555 1555 1.35 LINK O2 GAL D 1 C1 FUC D 2 1555 1555 1.45 LINK O3 GAL D 1 C1 A2G D 3 1555 1555 1.38 LINK O LYS A 137 CA CA A1213 1555 1555 2.31 LINK O ALA A 187 CA CA A1213 1555 1555 2.31 LINK O LYS A 190 CA CA A1213 1555 1555 2.29 LINK OD1 ASP A 194 CA CA A1213 1555 1555 2.78 LINK OD2 ASP A 194 CA CA A1213 1555 1555 2.35 LINK CA CA A1213 O HOH A2196 1555 1555 2.45 LINK CA CA A1213 O HOH A2276 1555 1555 2.42 LINK O LYS B 137 CA CA B1214 1555 1555 2.30 LINK O ALA B 187 CA CA B1214 1555 1555 2.30 LINK O LYS B 190 CA CA B1214 1555 1555 2.23 LINK OD1 ASP B 194 CA CA B1214 1555 1555 2.82 LINK OD2 ASP B 194 CA CA B1214 1555 1555 2.32 LINK CA CA B1214 O HOH B2179 1555 1555 2.50 LINK CA CA B1214 O HOH B2257 1555 1555 2.44 CISPEP 1 SER A 102 PRO A 103 0 -8.67 CISPEP 2 SER B 102 PRO B 103 0 -10.98 CRYST1 69.683 98.754 49.241 90.00 90.00 90.00 P 21 21 2 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 0.014351 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010126 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020308 0.00000