PDB Short entry for 2JDA HEADER SUGAR BINDING PROTEIN 05-JAN-07 2JDA TITLE STRUCTURE OF A PECTIN BINDING CARBOHYDRATE BINDING MODULE DETERMINED TITLE 2 IN AN MONOCLINIC CRYSTAL FORM. COMPND MOL_ID: 1; COMPND 2 MOLECULE: YECBM32; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA ENTEROCOLITICA; SOURCE 3 ORGANISM_TAXID: 630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET 28A KEYWDS HYPOTHETICAL PROTEIN, YERSINIA ENTEROCOLITICA, CARBOHYDRATE- BINDING KEYWDS 2 MODULE, SUGAR-BINDING PROTEIN, PECTIN, PLANT CELL WALL, GALACTURONIC KEYWDS 3 ACID, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.W.ABBOTT,A.B.BORASTON REVDAT 4 08-MAY-24 2JDA 1 LINK REVDAT 3 24-FEB-09 2JDA 1 VERSN REVDAT 2 27-MAR-07 2JDA 1 HEADER KEYWDS JRNL REVDAT 1 16-JAN-07 2JDA 0 JRNL AUTH D.W.ABBOTT,S.HRYNUIK,A.B.BORASTON JRNL TITL IDENTIFICATION AND CHARACTERIZATION OF A NOVEL PERIPLASMIC JRNL TITL 2 POLYGALACTURONIC ACID BINDING PROTEIN FROM YERSINIA JRNL TITL 3 ENTEROLITICA JRNL REF J.MOL.BIOL. V. 367 1023 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17292916 JRNL DOI 10.1016/J.JMB.2007.01.030 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 53514 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2858 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1511 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.8010 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.7980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2172 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 486 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.24000 REMARK 3 B22 (A**2) : 0.28000 REMARK 3 B33 (A**2) : -0.27000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.23000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.063 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.058 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.034 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.889 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2305 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2054 ; 0.008 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3123 ; 1.924 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4836 ; 1.282 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 287 ; 6.778 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 349 ; 0.201 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2495 ; 0.020 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 419 ; 0.036 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 390 ; 0.189 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2407 ; 0.260 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1385 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 328 ; 0.203 ; 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): 14 ; 0.160 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 84 ; 0.340 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 38 ; 0.387 ; 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): 1412 ; 1.693 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2286 ; 2.527 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 893 ; 3.410 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 833 ; 5.251 ; 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 : BABINET MODEL WITH 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 2JDA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1290031009. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 113.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL 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 : 56372 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 38.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.26000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 55.60250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.36450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.60250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.36450 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 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 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 GLY A 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 PRO A 5 REMARK 465 PHE A 6 REMARK 465 GLY B 1 REMARK 465 SER B 2 REMARK 465 HIS B 3 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 2077 O HOH B 2078 1.91 REMARK 500 O4 SO4 A 1151 O HOH A 2242 2.03 REMARK 500 O HOH B 2082 O HOH B 2160 2.07 REMARK 500 N HIS B 4 O HOH B 2005 2.08 REMARK 500 N HIS B 4 O HOH B 2004 2.11 REMARK 500 O HOH B 2177 O HOH B 2179 2.13 REMARK 500 O HOH B 2004 O HOH B 2005 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2056 O HOH A 2238 4645 1.21 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 PHE B 118 CZ PHE B 118 CE2 -0.114 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 37 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 69 NE - CZ - NH1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG B 69 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ASP B 97 CB - CG - OD1 ANGL. DEV. = 5.8 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 ALA B 96 -72.50 -142.30 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 A2017 DISTANCE = 6.91 ANGSTROMS REMARK 525 HOH A2052 DISTANCE = 5.94 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 A1146 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 28 O REMARK 620 2 ASP A 31 OD1 81.0 REMARK 620 3 ASP A 33 O 166.7 88.5 REMARK 620 4 THR A 36 OG1 87.8 70.7 81.1 REMARK 620 5 THR A 36 O 95.1 141.2 88.1 70.5 REMARK 620 6 ASN A 129 O 86.4 144.7 106.8 141.8 72.4 REMARK 620 7 GLU A 130 OE1 99.6 74.5 85.2 142.8 143.5 75.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1146 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 28 O REMARK 620 2 ASP B 31 OD1 81.0 REMARK 620 3 ASP B 33 O 167.4 89.3 REMARK 620 4 THR B 36 O 92.7 140.6 89.7 REMARK 620 5 THR B 36 OG1 89.1 71.1 80.1 69.9 REMARK 620 6 ASN B 129 O 85.8 145.5 106.7 71.3 140.6 REMARK 620 7 GLU B 130 OE2 99.3 75.6 85.9 143.5 143.9 75.3 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. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1146 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B1146 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1147 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1148 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1149 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1147 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1148 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1149 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1150 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1152 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1153 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1154 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JD9 RELATED DB: PDB REMARK 900 STRUCTURE OF A PECTIN BINDING CARBOHYDRATE BINDING MODULE REMARK 900 DETERMINED IN AN ORTHORHOMBIC CRYSTAL FORM. DBREF 2JDA A 1 145 PDB 2JDA 2JDA 1 145 DBREF 2JDA B 1 145 PDB 2JDA 2JDA 1 145 SEQRES 1 A 145 GLY SER HIS HIS PRO PHE THR ALA GLN ILE VAL ALA VAL SEQRES 2 A 145 THR ALA SER GLY TYR ASP SER GLU LYS GLY HIS VAL PRO SEQRES 3 A 145 ALA ASN ILE ALA ASP GLY ASP VAL LYS THR ARG TRP ALA SEQRES 4 A 145 ALA SER GLY GLU SER TRP VAL GLN LEU GLU LEU ASP LYS SEQRES 5 A 145 GLU GLN SER ILE GLU ASN ILE LEU ILE VAL PRO PHE LYS SEQRES 6 A 145 PRO THR GLU ARG LYS LEU LYS PHE SER ILE PHE TYR SER SEQRES 7 A 145 ASN ASP GLY LYS ASN TRP GLN PRO LEU ALA GLU GLY LEU SEQRES 8 A 145 GLU THR SER SER ALA ASP LYS ASN GLY GLU LYS LEU THR SEQRES 9 A 145 PHE THR PRO VAL THR ALA LYS TYR ILE LYS LEU ASP THR SEQRES 10 A 145 PHE GLY THR ASP VAL ASN ASN TRP SER ALA ILE ASN GLU SEQRES 11 A 145 ILE ALA ILE ASN SER ALA ALA ALA LEU PRO SER ARG ALA SEQRES 12 A 145 ILE LYS SEQRES 1 B 145 GLY SER HIS HIS PRO PHE THR ALA GLN ILE VAL ALA VAL SEQRES 2 B 145 THR ALA SER GLY TYR ASP SER GLU LYS GLY HIS VAL PRO SEQRES 3 B 145 ALA ASN ILE ALA ASP GLY ASP VAL LYS THR ARG TRP ALA SEQRES 4 B 145 ALA SER GLY GLU SER TRP VAL GLN LEU GLU LEU ASP LYS SEQRES 5 B 145 GLU GLN SER ILE GLU ASN ILE LEU ILE VAL PRO PHE LYS SEQRES 6 B 145 PRO THR GLU ARG LYS LEU LYS PHE SER ILE PHE TYR SER SEQRES 7 B 145 ASN ASP GLY LYS ASN TRP GLN PRO LEU ALA GLU GLY LEU SEQRES 8 B 145 GLU THR SER SER ALA ASP LYS ASN GLY GLU LYS LEU THR SEQRES 9 B 145 PHE THR PRO VAL THR ALA LYS TYR ILE LYS LEU ASP THR SEQRES 10 B 145 PHE GLY THR ASP VAL ASN ASN TRP SER ALA ILE ASN GLU SEQRES 11 B 145 ILE ALA ILE ASN SER ALA ALA ALA LEU PRO SER ARG ALA SEQRES 12 B 145 ILE LYS HET CA A1146 1 HET GOL A1147 6 HET GOL A1148 6 HET GOL A1149 6 HET GOL A1150 6 HET SO4 A1151 5 HET CA B1146 1 HET GOL B1147 6 HET GOL B1148 6 HET GOL B1149 6 HET GOL B1150 6 HET SO4 B1151 5 HET GOL B1152 6 HET GOL B1153 6 HET GOL B1154 6 HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 CA 2(CA 2+) FORMUL 4 GOL 11(C3 H8 O3) FORMUL 8 SO4 2(O4 S 2-) FORMUL 18 HOH *486(H2 O) HELIX 1 1 VAL A 25 ASP A 31 5 7 HELIX 2 2 VAL B 25 ASP B 31 5 7 SHEET 1 AA 3 ILE A 10 ALA A 15 0 SHEET 2 AA 3 SER A 44 PRO A 63 -1 O GLN A 47 N THR A 14 SHEET 3 AA 3 GLU A 101 THR A 120 -1 O GLU A 101 N ILE A 61 SHEET 1 AB 4 ILE A 10 ALA A 15 0 SHEET 2 AB 4 SER A 44 PRO A 63 -1 O GLN A 47 N THR A 14 SHEET 3 AB 4 TRP A 125 ILE A 133 -1 N ASN A 129 O VAL A 62 SHEET 4 AB 4 TRP A 38 SER A 41 -1 O TRP A 38 N ILE A 128 SHEET 1 BA 3 ILE B 10 ALA B 15 0 SHEET 2 BA 3 SER B 44 PRO B 63 -1 O GLN B 47 N THR B 14 SHEET 3 BA 3 GLU B 101 THR B 120 -1 O GLU B 101 N ILE B 61 SHEET 1 BB 4 ILE B 10 ALA B 15 0 SHEET 2 BB 4 SER B 44 PRO B 63 -1 O GLN B 47 N THR B 14 SHEET 3 BB 4 TRP B 125 ILE B 133 -1 N ASN B 129 O VAL B 62 SHEET 4 BB 4 TRP B 38 SER B 41 -1 O TRP B 38 N ILE B 128 LINK O ASN A 28 CA CA A1146 1555 1555 2.29 LINK OD1 ASP A 31 CA CA A1146 1555 1555 2.50 LINK O ASP A 33 CA CA A1146 1555 1555 2.30 LINK OG1 THR A 36 CA CA A1146 1555 1555 2.50 LINK O THR A 36 CA CA A1146 1555 1555 2.48 LINK O ASN A 129 CA CA A1146 1555 1555 2.39 LINK OE1 GLU A 130 CA CA A1146 1555 1555 2.44 LINK O ASN B 28 CA CA B1146 1555 1555 2.28 LINK OD1 ASP B 31 CA CA B1146 1555 1555 2.48 LINK O ASP B 33 CA CA B1146 1555 1555 2.30 LINK O THR B 36 CA CA B1146 1555 1555 2.46 LINK OG1 THR B 36 CA CA B1146 1555 1555 2.53 LINK O ASN B 129 CA CA B1146 1555 1555 2.39 LINK OE2 GLU B 130 CA CA B1146 1555 1555 2.38 SITE 1 AC1 6 ASN A 28 ASP A 31 ASP A 33 THR A 36 SITE 2 AC1 6 ASN A 129 GLU A 130 SITE 1 AC2 9 LYS A 102 PRO A 140 SER A 141 HOH A2240 SITE 2 AC2 9 HOH A2241 HOH A2242 HOH A2243 ARG B 142 SITE 3 AC2 9 HOH B2226 SITE 1 AC3 6 ASN B 28 ASP B 31 ASP B 33 THR B 36 SITE 2 AC3 6 ASN B 129 GLU B 130 SITE 1 AC4 6 ASN A 79 HOH A2140 LYS B 22 ASN B 83 SITE 2 AC4 6 HOH B2237 HOH B2238 SITE 1 AC5 8 VAL A 11 GLY A 17 ALA A 27 SER A 41 SITE 2 AC5 8 GOL A1148 GOL A1150 HOH A2026 HOH A2081 SITE 1 AC6 9 VAL A 11 TYR A 18 ALA A 40 SER A 41 SITE 2 AC6 9 GOL A1147 GOL A1150 HOH A2015 HOH A2233 SITE 3 AC6 9 HOH A2234 SITE 1 AC7 9 GLY A 23 VAL A 25 TRP A 45 GLN A 47 SITE 2 AC7 9 LYS A 114 HOH A2142 HOH A2235 HOH A2237 SITE 3 AC7 9 HOH A2238 SITE 1 AC8 9 GLY A 17 TYR A 18 SER A 20 GLU A 89 SITE 2 AC8 9 GOL A1147 GOL A1148 HOH A2027 HOH A2045 SITE 3 AC8 9 HOH A2155 SITE 1 AC9 9 VAL B 11 GLY B 17 ALA B 27 SER B 41 SITE 2 AC9 9 GOL B1148 GOL B1150 HOH B2027 HOH B2090 SITE 3 AC9 9 HOH B2229 SITE 1 BC1 9 VAL B 11 TYR B 18 ALA B 40 SER B 41 SITE 2 BC1 9 TRP B 125 GOL B1147 HOH B2230 HOH B2231 SITE 3 BC1 9 HOH B2232 SITE 1 BC2 8 GLY B 23 VAL B 25 TRP B 45 GLN B 47 SITE 2 BC2 8 LYS B 114 HOH B2233 HOH B2234 HOH B2235 SITE 1 BC3 6 GLY B 17 TYR B 18 SER B 20 GLU B 89 SITE 2 BC3 6 GOL B1147 HOH B2158 SITE 1 BC4 9 VAL A 108 THR A 109 HOH A2136 HOH A2188 SITE 2 BC4 9 TYR B 77 SER B 78 ASN B 79 ASN B 83 SITE 3 BC4 9 HOH B2188 SITE 1 BC5 10 THR A 104 PHE A 105 THR B 106 SER B 141 SITE 2 BC5 10 ARG B 142 ALA B 143 HOH B2220 HOH B2223 SITE 3 BC5 10 HOH B2239 HOH B2240 SITE 1 BC6 6 LYS B 65 ARG B 69 ASN B 123 TRP B 125 SITE 2 BC6 6 HOH B2242 HOH B2243 CRYST1 111.205 34.729 86.711 90.00 120.58 90.00 C 1 2 1 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 0.008992 0.000000 0.005314 0.00000 SCALE2 0.000000 0.028794 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013396 0.00000