HEADER SUGAR BINDING PROTEIN 26-JAN-15 4XUR TITLE STRUCTURE OF THE CBM22-2 XYLAN-BINDING DOMAIN FROM PAENIBACILLUS TITLE 2 BARCINONENSIS XYN10C IN COMPLEX WITH XYLOTETRAOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE C; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: UNP RESIDUES 186-366; COMPND 5 SYNONYM: XYLANASE C,1,4-BETA-D-XYLAN XYLANOHYDROLASE C, CBM22; COMPND 6 EC: 3.2.1.8; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PAENIBACILLUS BARCINONENSIS; SOURCE 3 ORGANISM_TAXID: 198119; SOURCE 4 GENE: XYNC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-2 KEYWDS BINDING SITE, CARBOHYDRATES, ENZYME STABILITY, SUBSTRATE SPECIFICITY, KEYWDS 2 ENDO-1, 4-BETA-XYLANASE, XYLAN-BINDING DOMAIN, THERMOPHILIC ENZYMES, KEYWDS 3 THERMOSTABILIZING DOMAINS, XYLOTETRAOSE, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SAINZ-POLO,J.SANZ-APARICIO REVDAT 5 10-JAN-24 4XUR 1 HETSYN LINK REVDAT 4 29-JUL-20 4XUR 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 18-APR-18 4XUR 1 JRNL REVDAT 2 22-JUL-15 4XUR 1 JRNL REVDAT 1 03-JUN-15 4XUR 0 JRNL AUTH M.A.SAINZ-POLO,B.GONZALEZ,M.MENENDEZ,F.I.PASTOR, JRNL AUTH 2 J.SANZ-APARICIO JRNL TITL EXPLORING MULTIMODULARITY IN PLANT CELL WALL DECONSTRUCTION: JRNL TITL 2 STRUCTURAL AND FUNCTIONAL ANALYSIS OF XYN10C CONTAINING THE JRNL TITL 3 CBM22-1-CBM22-2 TANDEM. JRNL REF J.BIOL.CHEM. V. 290 17116 2015 JRNL REFN ESSN 1083-351X JRNL PMID 26001782 JRNL DOI 10.1074/JBC.M115.659300 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.A.SAINZ-POLO,B.GONZALEZ,F.I.PASTOR,J.SANZ-APARICIO REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION ANALYSIS REMARK 1 TITL 2 OF THE N-TERMINAL DOMAIN OF PAENIBACILLUS BARCINONENSIS REMARK 1 TITL 3 XYLANASE 10C CONTAINING THE CBM22-1-CBM22-2 TANDEM. REMARK 1 REF ACTA CRYSTALLOGR F STRUCT V. 71 136 2015 REMARK 1 REF 2 BIOL COMMUN REMARK 1 REFN ESSN 2053-230X REMARK 1 PMID 25664784 REMARK 1 DOI 10.1107/S2053230X14027496 REMARK 2 REMARK 2 RESOLUTION. 1.67 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 51625 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2850 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) : 1.67 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.71 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3843 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.1670 REMARK 3 BIN FREE R VALUE SET COUNT : 213 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3789 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 104 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.54000 REMARK 3 B22 (A**2) : 0.54000 REMARK 3 B33 (A**2) : -1.07000 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): 0.019 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.019 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.283 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3974 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3641 ; 0.023 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5395 ; 1.622 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8415 ; 1.622 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 480 ; 7.236 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 180 ;35.387 ;24.833 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 645 ;13.947 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;23.828 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 617 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4410 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 882 ; 0.007 ; 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): 1929 ; 1.229 ; 1.569 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1928 ; 1.228 ; 1.568 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2406 ; 1.792 ; 2.347 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2407 ; 1.792 ; 2.348 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2045 ; 1.488 ; 1.720 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2046 ; 1.488 ; 1.720 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2990 ; 1.958 ; 2.534 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4307 ; 3.411 ;12.867 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4295 ; 3.393 ;12.867 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 : 3 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 172 332 B 172 332 9238 0.14 0.05 REMARK 3 2 A 172 332 C 172 332 9226 0.14 0.05 REMARK 3 3 B 172 332 C 172 332 9301 0.13 0.05 REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.537 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -K, -H, -L REMARK 3 TWIN FRACTION : 0.463 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 4XUR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000203681. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8729 REMARK 200 MONOCHROMATOR : HORIZONTALLY SIDE DIFFRACTING REMARK 200 SILICON 111 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54496 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 33.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : 0.04200 REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.45100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 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: 4XUN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.85M SODIUM MALONATE. RATIO REMARK 280 PROTEIN/PRECIPITANT=0.5/1, PH 6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,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 32.38067 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 16.19033 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, F 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 ALA A 159 REMARK 465 PRO A 160 REMARK 465 GLU A 161 REMARK 465 ASN A 162 REMARK 465 PRO A 163 REMARK 465 GLY A 164 REMARK 465 GLU A 165 REMARK 465 PRO A 166 REMARK 465 GLY A 167 REMARK 465 GLU A 168 REMARK 465 ALA A 169 REMARK 465 GLY A 170 REMARK 465 GLN A 171 REMARK 465 GLU A 333 REMARK 465 ALA A 334 REMARK 465 ILE A 335 REMARK 465 ALA A 336 REMARK 465 ILE A 337 REMARK 465 GLU A 338 REMARK 465 LYS A 339 REMARK 465 ALA B 159 REMARK 465 PRO B 160 REMARK 465 GLU B 161 REMARK 465 ASN B 162 REMARK 465 PRO B 163 REMARK 465 GLY B 164 REMARK 465 GLU B 165 REMARK 465 PRO B 166 REMARK 465 GLY B 167 REMARK 465 GLU B 168 REMARK 465 ALA B 169 REMARK 465 GLY B 170 REMARK 465 GLN B 171 REMARK 465 GLU B 333 REMARK 465 ALA B 334 REMARK 465 ILE B 335 REMARK 465 ALA B 336 REMARK 465 ILE B 337 REMARK 465 GLU B 338 REMARK 465 LYS B 339 REMARK 465 ALA C 159 REMARK 465 PRO C 160 REMARK 465 GLU C 161 REMARK 465 ASN C 162 REMARK 465 PRO C 163 REMARK 465 GLY C 164 REMARK 465 GLU C 165 REMARK 465 PRO C 166 REMARK 465 GLY C 167 REMARK 465 GLU C 168 REMARK 465 ALA C 169 REMARK 465 GLY C 170 REMARK 465 GLN C 171 REMARK 465 GLU C 333 REMARK 465 ALA C 334 REMARK 465 ILE C 335 REMARK 465 ALA C 336 REMARK 465 ILE C 337 REMARK 465 GLU C 338 REMARK 465 LYS C 339 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 O4 XYP F 3 C1 XYP C 1004 1.57 REMARK 500 O4 XYP E 2 C1 XYP B 1003 1.63 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 267 CD GLU A 267 OE2 -0.074 REMARK 500 TRP A 308 CB TRP A 308 CG -0.111 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 301 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 178 16.65 58.60 REMARK 500 LYS A 309 -82.03 -120.23 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 TRP A 308 LYS A 309 -54.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 XYP E 1 REMARK 610 XYP B 1003 REMARK 610 XYP C 1004 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 A1005 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 177 O REMARK 620 2 GLU A 179 OE2 84.6 REMARK 620 3 SER A 204 OG 154.9 76.7 REMARK 620 4 ARG A 206 O 99.4 80.7 94.0 REMARK 620 5 ASP A 325 OD1 77.0 158.6 124.0 91.6 REMARK 620 6 ASP A 325 OD2 129.4 144.2 73.1 82.6 52.5 REMARK 620 7 HOH A1133 O 95.0 97.1 71.2 165.2 95.2 91.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1004 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 177 O REMARK 620 2 GLU B 179 OE2 84.0 REMARK 620 3 SER B 204 OG 159.2 79.8 REMARK 620 4 ARG B 206 O 93.3 84.0 97.9 REMARK 620 5 ASP B 325 OD1 79.5 162.0 117.9 90.0 REMARK 620 6 ASP B 325 OD2 128.3 143.9 71.5 78.9 49.8 REMARK 620 7 HOH B1119 O 100.3 97.7 69.3 166.3 92.1 92.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C1005 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 177 O REMARK 620 2 GLU C 179 OE2 78.0 REMARK 620 3 SER C 204 OG 153.0 78.4 REMARK 620 4 ARG C 206 O 97.7 90.2 95.3 REMARK 620 5 ASP C 325 OD1 74.6 152.4 127.2 96.7 REMARK 620 6 ASP C 325 OD2 124.9 155.5 80.8 79.0 51.8 REMARK 620 7 HOH C1131 O 100.2 93.3 68.4 162.1 88.3 90.9 REMARK 620 N 1 2 3 4 5 6 REMARK 630 REMARK 630 MOLECULE TYPE: OLIGOSACCHARIDE METABOLISM REMARK 630 MOLECULE NAME: BETA-D-XYLOPYRANOSE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 XYP B 1003 REMARK 630 XYP C 1004 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: NULL REMARK 630 DETAILS: OLIGOSACCHARIDE DBREF 4XUR A 159 339 UNP O69230 XYNC_PAEBA 186 366 DBREF 4XUR B 159 339 UNP O69230 XYNC_PAEBA 186 366 DBREF 4XUR C 159 339 UNP O69230 XYNC_PAEBA 186 366 SEQADV 4XUR ASP A 177 UNP O69230 TYR 204 CONFLICT SEQADV 4XUR ASP B 177 UNP O69230 TYR 204 CONFLICT SEQADV 4XUR ASP C 177 UNP O69230 TYR 204 CONFLICT SEQRES 1 A 181 ALA PRO GLU ASN PRO GLY GLU PRO GLY GLU ALA GLY GLN SEQRES 2 A 181 ALA LEU PHE LYS ALA ASP PHE GLU ASP GLY ASN ILE GLY SEQRES 3 A 181 ASN TRP ARG ALA ARG GLY THR GLU LYS LEU GLU VAL VAL SEQRES 4 A 181 SER GLY ILE GLY HIS ASN SER ASN ARG SER LEU LYS THR SEQRES 5 A 181 SER SER ARG SER GLU THR TYR HIS GLY PRO LEU VAL GLU SEQRES 6 A 181 VAL LEU PRO TYR LEU GLN LYS GLY SER THR VAL HIS ILE SEQRES 7 A 181 SER PHE TRP ALA MET TYR ASP GLU GLY PRO ALA THR GLN SEQRES 8 A 181 VAL ILE ASN GLY SER LEU GLU LYS GLU PHE ASN ARG ASP SEQRES 9 A 181 THR ALA ASN LEU GLU TYR ALA MET PHE ALA SER THR THR SEQRES 10 A 181 LEU ASN LYS GLY GLN TRP LYS LYS ILE GLU ALA ASP ILE SEQRES 11 A 181 ILE VAL PRO ALA GLU SER THR GLY ILE SER GLY LEU ARG SEQRES 12 A 181 MET TYR ALA GLU THR PRO TRP LYS GLN SER SER GLU VAL SEQRES 13 A 181 THR GLU THR ASP THR ILE PRO PHE TYR VAL ASP ASP VAL SEQRES 14 A 181 GLN ILE THR ALA THR GLU ALA ILE ALA ILE GLU LYS SEQRES 1 B 181 ALA PRO GLU ASN PRO GLY GLU PRO GLY GLU ALA GLY GLN SEQRES 2 B 181 ALA LEU PHE LYS ALA ASP PHE GLU ASP GLY ASN ILE GLY SEQRES 3 B 181 ASN TRP ARG ALA ARG GLY THR GLU LYS LEU GLU VAL VAL SEQRES 4 B 181 SER GLY ILE GLY HIS ASN SER ASN ARG SER LEU LYS THR SEQRES 5 B 181 SER SER ARG SER GLU THR TYR HIS GLY PRO LEU VAL GLU SEQRES 6 B 181 VAL LEU PRO TYR LEU GLN LYS GLY SER THR VAL HIS ILE SEQRES 7 B 181 SER PHE TRP ALA MET TYR ASP GLU GLY PRO ALA THR GLN SEQRES 8 B 181 VAL ILE ASN GLY SER LEU GLU LYS GLU PHE ASN ARG ASP SEQRES 9 B 181 THR ALA ASN LEU GLU TYR ALA MET PHE ALA SER THR THR SEQRES 10 B 181 LEU ASN LYS GLY GLN TRP LYS LYS ILE GLU ALA ASP ILE SEQRES 11 B 181 ILE VAL PRO ALA GLU SER THR GLY ILE SER GLY LEU ARG SEQRES 12 B 181 MET TYR ALA GLU THR PRO TRP LYS GLN SER SER GLU VAL SEQRES 13 B 181 THR GLU THR ASP THR ILE PRO PHE TYR VAL ASP ASP VAL SEQRES 14 B 181 GLN ILE THR ALA THR GLU ALA ILE ALA ILE GLU LYS SEQRES 1 C 181 ALA PRO GLU ASN PRO GLY GLU PRO GLY GLU ALA GLY GLN SEQRES 2 C 181 ALA LEU PHE LYS ALA ASP PHE GLU ASP GLY ASN ILE GLY SEQRES 3 C 181 ASN TRP ARG ALA ARG GLY THR GLU LYS LEU GLU VAL VAL SEQRES 4 C 181 SER GLY ILE GLY HIS ASN SER ASN ARG SER LEU LYS THR SEQRES 5 C 181 SER SER ARG SER GLU THR TYR HIS GLY PRO LEU VAL GLU SEQRES 6 C 181 VAL LEU PRO TYR LEU GLN LYS GLY SER THR VAL HIS ILE SEQRES 7 C 181 SER PHE TRP ALA MET TYR ASP GLU GLY PRO ALA THR GLN SEQRES 8 C 181 VAL ILE ASN GLY SER LEU GLU LYS GLU PHE ASN ARG ASP SEQRES 9 C 181 THR ALA ASN LEU GLU TYR ALA MET PHE ALA SER THR THR SEQRES 10 C 181 LEU ASN LYS GLY GLN TRP LYS LYS ILE GLU ALA ASP ILE SEQRES 11 C 181 ILE VAL PRO ALA GLU SER THR GLY ILE SER GLY LEU ARG SEQRES 12 C 181 MET TYR ALA GLU THR PRO TRP LYS GLN SER SER GLU VAL SEQRES 13 C 181 THR GLU THR ASP THR ILE PRO PHE TYR VAL ASP ASP VAL SEQRES 14 C 181 GLN ILE THR ALA THR GLU ALA ILE ALA ILE GLU LYS HET XYP D 1 10 HET XYP D 2 9 HET XYP D 3 9 HET XYP D 4 9 HET XYP E 1 9 HET XYP E 2 9 HET XYP F 1 10 HET XYP F 2 9 HET XYP F 3 9 HET CA A1005 1 HET XYP B1003 9 HET CA B1004 1 HET XYP C1004 9 HET CA C1005 1 HETNAM XYP BETA-D-XYLOPYRANOSE HETNAM CA CALCIUM ION HETSYN XYP BETA-D-XYLOSE; D-XYLOSE; XYLOSE FORMUL 4 XYP 11(C5 H10 O5) FORMUL 7 CA 3(CA 2+) FORMUL 12 HOH *94(H2 O) HELIX 1 AA1 LEU A 225 LEU A 228 5 4 HELIX 2 AA2 ALA A 292 THR A 295 5 4 HELIX 3 AA3 GLN A 310 VAL A 314 5 5 HELIX 4 AA4 GLU A 316 ILE A 320 5 5 HELIX 5 AA5 LEU B 225 LEU B 228 5 4 HELIX 6 AA6 ALA B 292 THR B 295 5 4 HELIX 7 AA7 GLN B 310 VAL B 314 5 5 HELIX 8 AA8 LEU C 225 LEU C 228 5 4 HELIX 9 AA9 ALA C 292 THR C 295 5 4 HELIX 10 AB1 GLN C 310 VAL C 314 5 5 SHEET 1 AA1 4 PHE A 174 ALA A 176 0 SHEET 2 AA1 4 PHE A 322 ALA A 331 -1 O VAL A 327 N ALA A 176 SHEET 3 AA1 4 ARG A 206 SER A 211 -1 N THR A 210 O PHE A 322 SHEET 4 AA1 4 LYS A 193 SER A 198 -1 N LYS A 193 O SER A 211 SHEET 1 AA2 4 PHE A 174 ALA A 176 0 SHEET 2 AA2 4 PHE A 322 ALA A 331 -1 O VAL A 327 N ALA A 176 SHEET 3 AA2 4 THR A 233 MET A 241 -1 N MET A 241 O TYR A 323 SHEET 4 AA2 4 LYS A 282 ILE A 289 -1 O ILE A 284 N PHE A 238 SHEET 1 AA3 4 LEU A 221 GLU A 223 0 SHEET 2 AA3 4 ILE A 297 GLU A 305 -1 O MET A 302 N VAL A 222 SHEET 3 AA3 4 THR A 248 PHE A 259 -1 N SER A 254 O TYR A 303 SHEET 4 AA3 4 GLU A 267 ASN A 277 -1 O ALA A 272 N GLY A 253 SHEET 1 AA4 4 PHE B 174 ALA B 176 0 SHEET 2 AA4 4 PHE B 322 ALA B 331 -1 O VAL B 327 N ALA B 176 SHEET 3 AA4 4 ARG B 206 SER B 211 -1 N THR B 210 O PHE B 322 SHEET 4 AA4 4 LYS B 193 SER B 198 -1 N LYS B 193 O SER B 211 SHEET 1 AA5 4 PHE B 174 ALA B 176 0 SHEET 2 AA5 4 PHE B 322 ALA B 331 -1 O VAL B 327 N ALA B 176 SHEET 3 AA5 4 THR B 233 MET B 241 -1 N MET B 241 O TYR B 323 SHEET 4 AA5 4 LYS B 282 ILE B 289 -1 O ILE B 288 N VAL B 234 SHEET 1 AA6 4 LEU B 221 GLU B 223 0 SHEET 2 AA6 4 ILE B 297 GLU B 305 -1 O MET B 302 N VAL B 222 SHEET 3 AA6 4 THR B 248 PHE B 259 -1 N GLU B 258 O SER B 298 SHEET 4 AA6 4 GLU B 267 ASN B 277 -1 O ALA B 272 N GLY B 253 SHEET 1 AA7 4 PHE C 174 ALA C 176 0 SHEET 2 AA7 4 PHE C 322 ALA C 331 -1 O VAL C 327 N ALA C 176 SHEET 3 AA7 4 ARG C 206 SER C 211 -1 N THR C 210 O PHE C 322 SHEET 4 AA7 4 LYS C 193 SER C 198 -1 N GLU C 195 O LYS C 209 SHEET 1 AA8 4 PHE C 174 ALA C 176 0 SHEET 2 AA8 4 PHE C 322 ALA C 331 -1 O VAL C 327 N ALA C 176 SHEET 3 AA8 4 THR C 233 MET C 241 -1 N SER C 237 O GLN C 328 SHEET 4 AA8 4 LYS C 282 ILE C 289 -1 O ILE C 288 N VAL C 234 SHEET 1 AA9 4 LEU C 221 GLU C 223 0 SHEET 2 AA9 4 ILE C 297 GLU C 305 -1 O MET C 302 N VAL C 222 SHEET 3 AA9 4 THR C 248 PHE C 259 -1 N ASN C 252 O GLU C 305 SHEET 4 AA9 4 GLU C 267 ASN C 277 -1 O PHE C 271 N GLY C 253 LINK O4 XYP D 1 C1 XYP D 2 1555 1555 1.53 LINK O4 XYP D 2 C1 XYP D 3 1555 1555 1.41 LINK O4 XYP D 3 C1 XYP D 4 1555 1555 1.46 LINK O4 XYP E 1 C1 XYP E 2 1555 1555 1.42 LINK O4 XYP F 1 C1 XYP F 2 1555 1555 1.52 LINK O4 XYP F 2 C1 XYP F 3 1555 1555 1.40 LINK O ASP A 177 CA CA A1005 1555 1555 2.39 LINK OE2 GLU A 179 CA CA A1005 1555 1555 2.35 LINK OG SER A 204 CA CA A1005 1555 1555 2.63 LINK O ARG A 206 CA CA A1005 1555 1555 2.31 LINK OD1 ASP A 325 CA CA A1005 1555 1555 2.47 LINK OD2 ASP A 325 CA CA A1005 1555 1555 2.53 LINK CA CA A1005 O HOH A1133 1555 1555 2.20 LINK O ASP B 177 CA CA B1004 1555 1555 2.34 LINK OE2 GLU B 179 CA CA B1004 1555 1555 2.30 LINK OG SER B 204 CA CA B1004 1555 1555 2.57 LINK O ARG B 206 CA CA B1004 1555 1555 2.36 LINK OD1 ASP B 325 CA CA B1004 1555 1555 2.48 LINK OD2 ASP B 325 CA CA B1004 1555 1555 2.68 LINK CA CA B1004 O HOH B1119 1555 1555 2.33 LINK O ASP C 177 CA CA C1005 1555 1555 2.49 LINK OE2 GLU C 179 CA CA C1005 1555 1555 2.43 LINK OG SER C 204 CA CA C1005 1555 1555 2.51 LINK O ARG C 206 CA CA C1005 1555 1555 2.27 LINK OD1 ASP C 325 CA CA C1005 1555 1555 2.60 LINK OD2 ASP C 325 CA CA C1005 1555 1555 2.41 LINK CA CA C1005 O HOH C1131 1555 1555 2.41 CISPEP 1 LYS A 309 GLN A 310 0 -13.86 CRYST1 92.769 92.769 48.571 90.00 90.00 120.00 P 32 9 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 0.010779 0.006224 0.000000 0.00000 SCALE2 0.000000 0.012447 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020589 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.604259 0.793010 -0.077503 -5.63238 1 MTRIX2 2 0.764592 -0.604464 -0.223657 -53.93146 1 MTRIX3 2 -0.224210 0.075888 -0.971582 17.03236 1 MTRIX1 3 0.985603 -0.169075 0.000852 -41.17363 1 MTRIX2 3 0.168735 0.983915 0.058647 -34.43835 1 MTRIX3 3 -0.010754 -0.057658 0.998278 13.70299 1