HEADER HYDROLASE 20-AUG-10 2XON TITLE STRUCTURE OF TMCBM61 IN COMPLEX WITH BETA-1,4-GALACTOTRIOSE AT 1.4 A TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARABINOGALACTAN ENDO-1,4-BETA-GALACTOSIDASE; COMPND 3 CHAIN: A, L; COMPND 4 FRAGMENT: CARBOHYDRATE-BINDING MODULES, RESIDUES 461-606; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 STRAIN: MS8B; SOURCE 5 ATCC: 43589; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PCBM61 KEYWDS HYDROLASE, GALACTAN, CARBOHYDRATE-BINDING MODULE, GLYCOSIDE KEYWDS 2 HYDROLASE, BETA-SANDWICH. EXPDTA X-RAY DIFFRACTION AUTHOR M.CID,H.LODBERG-PEDERSEN,S.KANEKO,P.M.COUTINHO,B.HENRISSAT, AUTHOR 2 W.G.T.WILLATS,A.B.BORASTON REVDAT 4 20-DEC-23 2XON 1 HETSYN REVDAT 3 29-JUL-20 2XON 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 18-MAY-11 2XON 1 JRNL REVDAT 1 08-SEP-10 2XON 0 JRNL AUTH M.CID,H.L.PEDERSEN,S.KANEKO,P.M.COUTINHO,B.HENRISSAT, JRNL AUTH 2 W.G.T.WILLATS,A.B.BORASTON JRNL TITL RECOGNITION OF THE HELICAL STRUCTURE OF BETA-1,4-GALACTAN BY JRNL TITL 2 A NEW FAMILY OF CARBOHYDRATE-BINDING MODULES. JRNL REF J.BIOL.CHEM. V. 285 35999 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20826814 JRNL DOI 10.1074/JBC.M110.166330 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 34.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 56801 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) : 0.119 REMARK 3 R VALUE (WORKING SET) : 0.116 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3009 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) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3060 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.1360 REMARK 3 BIN FREE R VALUE SET COUNT : 158 REMARK 3 BIN FREE R VALUE : 0.2010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2350 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 179 REMARK 3 SOLVENT ATOMS : 553 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.058 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.058 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.030 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.648 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2738 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1976 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3703 ; 2.184 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4768 ; 1.098 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 335 ; 7.339 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;31.869 ;24.015 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 448 ;13.029 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;13.738 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 395 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2962 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 581 ; 0.002 ; 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): 1516 ; 2.252 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 628 ; 1.235 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2472 ; 3.124 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1222 ; 4.325 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1205 ; 5.773 ; 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): 4713 ; 2.277 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 555 ;13.348 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4645 ; 6.417 ; 3.000 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. U VALUES REFINED INDIVIDUALLY. REMARK 4 REMARK 4 2XON COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1290045099. 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 : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56801 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 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 (%) : 95.3 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.4000 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) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.18000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2XOM REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.92500 REMARK 290 SMTRY3 2 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: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, 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 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 15 REMARK 465 SER A 16 REMARK 465 HIS A 17 REMARK 465 MET A 18 REMARK 465 ALA A 19 REMARK 465 SER A 20 REMARK 465 GLU A 166 REMARK 465 GLY L 15 REMARK 465 SER L 16 REMARK 465 HIS L 17 REMARK 465 MET L 18 REMARK 465 ALA L 19 REMARK 465 SER L 20 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 GLU L 97 O 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 ND2 ASN L 133 O HOH L 2210 1.50 REMARK 500 O2 EDO A 1168 O HOH A 2259 1.83 REMARK 500 OE1 GLU A 71 O HOH A 2128 1.87 REMARK 500 N SER A 21 O HOH A 2004 1.87 REMARK 500 OE1 GLU L 117 O HOH L 2181 2.07 REMARK 500 OE2 GLU L 166 O HOH L 2240 2.09 REMARK 500 O HOH L 2154 O HOH L 2156 2.11 REMARK 500 O HOH L 2206 O HOH L 2211 2.11 REMARK 500 O2 EDO A 1171 O HOH A 2263 2.14 REMARK 500 O HOH L 2154 O HOH L 2155 2.14 REMARK 500 O2 EDO A 1176 O HOH A 2270 2.15 REMARK 500 O2 EDO A 1185 O HOH A 2276 2.15 REMARK 500 O HOH L 2155 O HOH L 2243 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 OE1 GLU A 80 O2 EDO L 1180 1556 1.88 REMARK 500 NZ LYS A 142 C1 EDO L 1172 2656 2.16 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 SER A 21 CB SER A 21 OG 0.089 REMARK 500 GLU A 71 CG GLU A 71 CD 0.106 REMARK 500 GLU A 71 CD GLU A 71 OE2 0.077 REMARK 500 GLU L 82 CD GLU L 82 OE2 -0.160 REMARK 500 GLU L 166 CD GLU L 166 OE1 0.066 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 GLU L 97 CA - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 ARG L 132 NE - CZ - NH1 ANGL. DEV. = -3.1 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 ASN A 27 52.86 39.82 REMARK 500 TRP A 68 146.98 -176.77 REMARK 500 TRP L 68 147.12 -176.22 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 GLU L 165 GLU L 166 139.57 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 A2044 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH L2039 DISTANCE = 5.87 ANGSTROMS 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 EDO L 1177 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 A1166 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 29 O REMARK 620 2 GLU A 31 OE2 82.1 REMARK 620 3 GLN A 60 OE1 88.6 88.2 REMARK 620 4 GLN A 60 O 160.0 84.2 76.5 REMARK 620 5 TYR A 63 O 88.3 85.1 172.9 105.0 REMARK 620 6 ASP A 158 OD1 124.1 149.0 107.0 73.8 80.0 REMARK 620 7 ASP A 158 OD2 76.3 157.8 96.3 118.1 89.1 49.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA L1170 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY L 29 O REMARK 620 2 GLU L 31 OE2 82.0 REMARK 620 3 GLN L 60 OE1 89.1 91.1 REMARK 620 4 GLN L 60 O 161.4 84.7 78.2 REMARK 620 5 TYR L 63 O 87.6 83.9 174.4 103.9 REMARK 620 6 ASP L 158 OD1 124.2 148.6 105.0 72.8 80.6 REMARK 620 7 ASP L 158 OD2 75.3 156.5 94.7 118.8 88.9 50.3 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XOM RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF TMCBM61 IN COMPLEX WITH BETA-1,4- REMARK 900 GALACTOTRIOSE DBREF 2XON A 21 166 UNP Q9X0S8 Q9X0S8_THEMA 461 606 DBREF 2XON L 21 166 UNP Q9X0S8 Q9X0S8_THEMA 461 606 SEQADV 2XON GLY A 15 UNP Q9X0S8 EXPRESSION TAG SEQADV 2XON SER A 16 UNP Q9X0S8 EXPRESSION TAG SEQADV 2XON HIS A 17 UNP Q9X0S8 EXPRESSION TAG SEQADV 2XON MET A 18 UNP Q9X0S8 EXPRESSION TAG SEQADV 2XON ALA A 19 UNP Q9X0S8 EXPRESSION TAG SEQADV 2XON SER A 20 UNP Q9X0S8 EXPRESSION TAG SEQADV 2XON GLY L 15 UNP Q9X0S8 EXPRESSION TAG SEQADV 2XON SER L 16 UNP Q9X0S8 EXPRESSION TAG SEQADV 2XON HIS L 17 UNP Q9X0S8 EXPRESSION TAG SEQADV 2XON MET L 18 UNP Q9X0S8 EXPRESSION TAG SEQADV 2XON ALA L 19 UNP Q9X0S8 EXPRESSION TAG SEQADV 2XON SER L 20 UNP Q9X0S8 EXPRESSION TAG SEQRES 1 A 152 GLY SER HIS MET ALA SER SER ARG ASN TYR LEU LYS ASN SEQRES 2 A 152 PRO GLY PHE GLU THR GLY GLU PHE SER PRO TRP ARG VAL SEQRES 3 A 152 SER GLY ASP LYS LYS ALA VAL LYS VAL VAL LYS ALA ASN SEQRES 4 A 152 PRO SER SER ASN ALA HIS GLN GLY GLU TYR ALA VAL ASN SEQRES 5 A 152 PHE TRP LEU ASP GLU SER PHE SER PHE GLU LEU SER GLN SEQRES 6 A 152 GLU VAL GLU LEU PRO ALA GLY VAL TYR ARG VAL GLY PHE SEQRES 7 A 152 TRP THR HIS GLY GLU LYS GLY VAL LYS ILE ALA LEU LYS SEQRES 8 A 152 VAL SER ASP TYR GLY GLY ASN GLU ARG SER VAL GLU VAL SEQRES 9 A 152 GLU THR THR GLY TRP LEU GLU TRP LYS ASN PRO GLU ILE SEQRES 10 A 152 ARG ASN ILE LYS VAL GLU THR GLY ARG ILE LYS ILE THR SEQRES 11 A 152 VAL SER VAL GLU GLY ARG ALA GLY ASP TRP GLY PHE ILE SEQRES 12 A 152 ASP ASP PHE TYR LEU PHE ARG GLU GLU SEQRES 1 L 152 GLY SER HIS MET ALA SER SER ARG ASN TYR LEU LYS ASN SEQRES 2 L 152 PRO GLY PHE GLU THR GLY GLU PHE SER PRO TRP ARG VAL SEQRES 3 L 152 SER GLY ASP LYS LYS ALA VAL LYS VAL VAL LYS ALA ASN SEQRES 4 L 152 PRO SER SER ASN ALA HIS GLN GLY GLU TYR ALA VAL ASN SEQRES 5 L 152 PHE TRP LEU ASP GLU SER PHE SER PHE GLU LEU SER GLN SEQRES 6 L 152 GLU VAL GLU LEU PRO ALA GLY VAL TYR ARG VAL GLY PHE SEQRES 7 L 152 TRP THR HIS GLY GLU LYS GLY VAL LYS ILE ALA LEU LYS SEQRES 8 L 152 VAL SER ASP TYR GLY GLY ASN GLU ARG SER VAL GLU VAL SEQRES 9 L 152 GLU THR THR GLY TRP LEU GLU TRP LYS ASN PRO GLU ILE SEQRES 10 L 152 ARG ASN ILE LYS VAL GLU THR GLY ARG ILE LYS ILE THR SEQRES 11 L 152 VAL SER VAL GLU GLY ARG ALA GLY ASP TRP GLY PHE ILE SEQRES 12 L 152 ASP ASP PHE TYR LEU PHE ARG GLU GLU HET GAL B 1 12 HET GAL B 2 11 HET GAL B 3 11 HET GAL C 1 12 HET GAL C 2 11 HET GAL C 3 11 HET CA A1166 1 HET SO4 A1167 5 HET EDO A1168 4 HET EDO A1169 4 HET EDO A1170 4 HET EDO A1171 4 HET EDO A1172 4 HET EDO A1173 4 HET EDO A1174 4 HET EDO A1175 4 HET EDO A1176 4 HET EDO A1177 4 HET EDO A1178 4 HET EDO A1179 4 HET EDO A1183 4 HET EDO A1184 4 HET EDO A1185 4 HET EDO L1180 4 HET CA L1170 1 HET SO4 L1171 5 HET EDO L1172 4 HET EDO L1173 4 HET EDO L1174 4 HET EDO L1175 4 HET EDO L1176 4 HET EDO L1177 3 HET EDO L1178 4 HET EDO L1179 4 HET EDO L1181 4 HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 GAL 6(C6 H12 O6) FORMUL 5 CA 2(CA 2+) FORMUL 6 SO4 2(O4 S 2-) FORMUL 7 EDO 25(C2 H6 O2) FORMUL 34 HOH *553(H2 O) HELIX 1 1 PRO A 54 ALA A 58 5 5 HELIX 2 2 PRO L 54 ALA L 58 5 5 SHEET 1 AA 5 ARG A 39 GLY A 42 0 SHEET 2 AA 5 PHE A 73 GLU A 82 -1 O GLU A 76 N SER A 41 SHEET 3 AA 5 ARG A 140 GLY A 149 -1 O ILE A 141 N VAL A 81 SHEET 4 AA 5 LYS A 101 SER A 107 -1 O LYS A 101 N GLU A 148 SHEET 5 AA 5 ARG A 114 GLU A 119 -1 O ARG A 114 N VAL A 106 SHEET 1 AB 5 VAL A 47 LYS A 51 0 SHEET 2 AB 5 TYR A 63 TRP A 68 -1 O ALA A 64 N VAL A 50 SHEET 3 AB 5 TRP A 154 ARG A 164 -1 O GLY A 155 N PHE A 67 SHEET 4 AB 5 GLY A 86 GLY A 96 -1 O ARG A 89 N PHE A 163 SHEET 5 AB 5 GLY A 122 LYS A 127 -1 N GLY A 122 O GLY A 96 SHEET 1 AC 5 VAL A 47 LYS A 51 0 SHEET 2 AC 5 TYR A 63 TRP A 68 -1 O ALA A 64 N VAL A 50 SHEET 3 AC 5 TRP A 154 ARG A 164 -1 O GLY A 155 N PHE A 67 SHEET 4 AC 5 GLY A 86 GLY A 96 -1 O ARG A 89 N PHE A 163 SHEET 5 AC 5 GLU A 130 VAL A 136 -1 O ILE A 131 N VAL A 90 SHEET 1 AD 2 GLY A 122 LYS A 127 0 SHEET 2 AD 2 GLY A 86 GLY A 96 -1 O THR A 94 N LYS A 127 SHEET 1 LA 5 ARG L 39 GLY L 42 0 SHEET 2 LA 5 PHE L 73 GLU L 82 -1 O GLU L 76 N SER L 41 SHEET 3 LA 5 ARG L 140 GLY L 149 1 O ILE L 141 N VAL L 81 SHEET 4 LA 5 GLY L 86 SER L 107 -1 O LYS L 101 N GLU L 148 SHEET 5 LA 5 ARG L 114 LYS L 127 -1 O ARG L 114 N VAL L 106 SHEET 1 LB 7 ARG L 39 GLY L 42 0 SHEET 2 LB 7 PHE L 73 GLU L 82 -1 O GLU L 76 N SER L 41 SHEET 3 LB 7 ARG L 140 GLY L 149 1 O ILE L 141 N VAL L 81 SHEET 4 LB 7 GLY L 86 SER L 107 -1 O LYS L 101 N GLU L 148 SHEET 5 LB 7 TRP L 154 ARG L 164 -1 O PHE L 156 N HIS L 95 SHEET 6 LB 7 TYR L 63 TRP L 68 -1 O VAL L 65 N ILE L 157 SHEET 7 LB 7 VAL L 47 LYS L 51 -1 O LYS L 48 N ASN L 66 SHEET 1 LC 5 ARG L 39 GLY L 42 0 SHEET 2 LC 5 PHE L 73 GLU L 82 -1 O GLU L 76 N SER L 41 SHEET 3 LC 5 ARG L 140 GLY L 149 1 O ILE L 141 N VAL L 81 SHEET 4 LC 5 GLY L 86 SER L 107 -1 O LYS L 101 N GLU L 148 SHEET 5 LC 5 GLU L 130 VAL L 136 -1 O ILE L 131 N VAL L 90 SHEET 1 LD 2 ARG L 114 LYS L 127 0 SHEET 2 LD 2 GLY L 86 SER L 107 -1 O THR L 94 N LYS L 127 LINK O4 GAL B 1 C1 GAL B 2 1555 1555 1.38 LINK O4 GAL B 2 C1 GAL B 3 1555 1555 1.38 LINK O4 GAL C 1 C1 GAL C 2 1555 1555 1.45 LINK O4 GAL C 2 C1 GAL C 3 1555 1555 1.40 LINK O GLY A 29 CA CA A1166 1555 1555 2.43 LINK OE2 GLU A 31 CA CA A1166 1555 1555 2.30 LINK OE1 GLN A 60 CA CA A1166 1555 1555 2.31 LINK O GLN A 60 CA CA A1166 1555 1555 2.43 LINK O TYR A 63 CA CA A1166 1555 1555 2.31 LINK OD1 ASP A 158 CA CA A1166 1555 1555 2.66 LINK OD2 ASP A 158 CA CA A1166 1555 1555 2.44 LINK O GLY L 29 CA CA L1170 1555 1555 2.42 LINK OE2 GLU L 31 CA CA L1170 1555 1555 2.30 LINK OE1 GLN L 60 CA CA L1170 1555 1555 2.31 LINK O GLN L 60 CA CA L1170 1555 1555 2.41 LINK O TYR L 63 CA CA L1170 1555 1555 2.29 LINK OD1 ASP L 158 CA CA L1170 1555 1555 2.70 LINK OD2 ASP L 158 CA CA L1170 1555 1555 2.45 CISPEP 1 SER A 36 PRO A 37 0 7.85 CISPEP 2 ASN A 53 PRO A 54 0 6.98 CISPEP 3 SER L 36 PRO L 37 0 4.54 CISPEP 4 ASN L 53 PRO L 54 0 4.95 CRYST1 48.900 61.850 55.530 90.00 105.14 90.00 P 1 21 1 4 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 0.020450 0.000000 0.005533 0.00000 SCALE2 0.000000 0.016168 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018656 0.00000