HEADER CARBOHYDRATE-BINDING MODULE 03-FEB-00 1DYO TITLE XYLAN-BINDING DOMAIN FROM CBM 22, FORMALLY X6B DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE Y; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: XYLAN-BINDING DOMAIN; COMPND 5 SYNONYM: CBM 22, X6B DOMAIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM THERMOCELLUM; SOURCE 3 ORGANISM_TAXID: 1515; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CARBOHYDRATE-BINDING MODULE, XYLAN-BINDING, XYLANASE EXPDTA X-RAY DIFFRACTION AUTHOR G.J.DAVIES,S.J.CHARNOCK,H.J.GILBERT,C.M.G.A.FONTES REVDAT 5 20-NOV-24 1DYO 1 REMARK LINK REVDAT 4 24-JUL-19 1DYO 1 REMARK LINK REVDAT 3 24-FEB-09 1DYO 1 JRNL REMARK DBREF SEQADV REVDAT 3 2 1 HETNAM FORMUL LINK HETATM REVDAT 3 3 1 CONECT REVDAT 2 11-MAR-04 1DYO 1 REVDAT 1 04-JUL-00 1DYO 0 JRNL AUTH S.J.CHARNOCK,D.N.BOLAM,J.P.TURKENBURG,H.J.GILBERT, JRNL AUTH 2 L.M.A.FERREIRA,G.J.DAVIES,C.M.G.A.FONTES JRNL TITL THE X6 THERMOSTABILISING DOMAINS OF XYLANASES ARE JRNL TITL 2 CARBOHYDRATE BINDING MODULES: STRUCTURE AND BIOCHEMISTRY OF JRNL TITL 3 THE CLOSTRIDIUM THERMOCELLUM X6B DOMAIN JRNL REF BIOCHEMISTRY V. 39 5013 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10819965 JRNL DOI 10.1021/BI992821Q REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 27951 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 448 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2432 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 297 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.012 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.036 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.036 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.012 ; 0.050 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.128 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.183 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.233 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.500 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 14.900; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 29.500; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.400 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.900 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.900 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.600 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FOR BOTH CHAINS THE FIRST 4 N- TERMINAL REMARK 3 RESIDUES ARE DISORDERED REMARK 4 REMARK 4 1DYO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-FEB-00. REMARK 100 THE DEPOSITION ID IS D_1290004587. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8445 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 141380 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.120 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 5.110 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : 0.07400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.43700 REMARK 200 R SYM FOR SHELL (I) : 0.43700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN FROM A PROTEIN REMARK 280 CONCENTRATION OF 50 MG/ML IN 0.1 M NAAC BUFFER, PH 4.6, REMARK 280 CONTAINING 10 MM DTT, 25 % (V/V) GLYCEROL AND WITH 12 % (W/V) REMARK 280 PEG 8000 AS THE PRECIPITANT, PH 4.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 69.23000 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 138.46000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 103.84500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 173.07500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 34.61500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.23000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 138.46000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 173.07500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 103.84500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 34.61500 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 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 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 LYS A 1 REMARK 465 PRO A 2 REMARK 465 GLU A 3 REMARK 465 GLU A 4 REMARK 465 LYS B 1 REMARK 465 PRO B 2 REMARK 465 GLU B 3 REMARK 465 GLU B 4 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 2094 O HOH A 2096 12556 2.14 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 MSE A 90 SE MSE A 90 CE -0.694 REMARK 500 MSE A 133 SE MSE A 133 CE -0.806 REMARK 500 MSE B 133 SE MSE B 133 CE -0.752 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 ASP A 6 CB - CG - OD1 ANGL. DEV. = -6.9 DEGREES REMARK 500 ASP A 6 N - CA - C ANGL. DEV. = 17.1 DEGREES REMARK 500 ASP A 6 O - C - N ANGL. DEV. = -12.7 DEGREES REMARK 500 ALA A 7 C - N - CA ANGL. DEV. = 22.6 DEGREES REMARK 500 ALA A 7 CA - C - O ANGL. DEV. = 17.3 DEGREES REMARK 500 GLY A 8 C - N - CA ANGL. DEV. = 17.4 DEGREES REMARK 500 LEU A 31 CA - CB - CG ANGL. DEV. = 14.8 DEGREES REMARK 500 GLU A 81 OE1 - CD - OE2 ANGL. DEV. = -8.5 DEGREES REMARK 500 ARG A 102 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 125 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 MSE A 133 CG - SE - CE ANGL. DEV. = 22.1 DEGREES REMARK 500 TYR A 134 CB - CG - CD2 ANGL. DEV. = 4.6 DEGREES REMARK 500 ASP B 6 CA - CB - CG ANGL. DEV. = 15.4 DEGREES REMARK 500 TYR B 9 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 TYR B 9 CB - CG - CD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 GLU B 16 OE1 - CD - OE2 ANGL. DEV. = -7.6 DEGREES REMARK 500 LEU B 31 CA - CB - CG ANGL. DEV. = 18.8 DEGREES REMARK 500 ARG B 35 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 TYR B 38 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG B 49 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 49 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG B 58 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP B 96 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 102 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 MSE B 133 CG - SE - CE ANGL. DEV. = 19.0 DEGREES REMARK 500 TYR B 147 CB - CG - CD1 ANGL. DEV. = -3.8 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 ASP A 6 -104.85 177.03 REMARK 500 SER A 18 134.44 -174.28 REMARK 500 ALA A 28 -171.46 -61.86 REMARK 500 ASP A 141 58.41 -153.86 REMARK 500 ASP B 6 -130.73 177.70 REMARK 500 PHE B 15 18.51 58.67 REMARK 500 ALA B 28 -179.38 -67.66 REMARK 500 PRO B 67 128.99 -39.41 REMARK 500 ASP B 141 47.88 -158.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP A 6 16.32 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 B2004 DISTANCE = 6.28 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 A 300 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 14 O REMARK 620 2 GLU A 16 OE2 89.0 REMARK 620 3 LYS A 39 O 156.0 90.0 REMARK 620 4 GLU A 42 O 105.7 91.6 98.3 REMARK 620 5 ASP A 149 OD2 113.5 157.1 71.4 78.6 REMARK 620 6 ASP A 149 OD1 70.7 159.6 109.3 92.3 42.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 300 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 14 O REMARK 620 2 GLU B 16 OE2 88.7 REMARK 620 3 LYS B 39 O 159.5 77.4 REMARK 620 4 GLU B 42 O 93.9 80.3 98.5 REMARK 620 5 ASP B 149 OD1 79.8 165.1 116.1 91.0 REMARK 620 6 ASP B 149 OD2 125.4 141.7 73.1 80.4 46.4 REMARK 620 7 HOH B2147 O 84.6 94.3 81.5 174.5 93.9 104.8 REMARK 620 N 1 2 3 4 5 6 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: REMARK 700 THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. REMARK 700 EACH IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE REMARK 700 IDENTICAL STRANDS. REMARK 700 SHEETS A AND A1 REPRESENT ONE BIFURCATED SHEET IN CHAIN A REMARK 700 SHEETS C AND C1 REPRESENT ONE BIFURCATED SHEET IN CHAIN B REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 300 REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE ASN 565 FROM SWISSPROT ENTRY P51584 IS DELETED REMARK 999 FROM THE PDB ENTRY DBREF 1DYO A 1 7 UNP P51584 XYNY_CLOTM 558 564 DBREF 1DYO A 8 160 UNP P51584 XYNY_CLOTM 566 718 DBREF 1DYO B 1 7 UNP P51584 XYNY_CLOTM 558 564 DBREF 1DYO B 8 160 UNP P51584 XYNY_CLOTM 566 718 SEQRES 1 A 160 LYS PRO GLU GLU PRO ASP ALA GLY TYR TYR TYR HIS ASP SEQRES 2 A 160 THR PHE GLU GLY SER VAL GLY GLN TRP THR ALA ARG GLY SEQRES 3 A 160 PRO ALA GLU VAL LEU LEU SER GLY ARG THR ALA TYR LYS SEQRES 4 A 160 GLY SER GLU SER LEU LEU VAL ARG ASN ARG THR ALA ALA SEQRES 5 A 160 TRP ASN GLY ALA GLN ARG ALA LEU ASN PRO ARG THR PHE SEQRES 6 A 160 VAL PRO GLY ASN THR TYR CYS PHE SER VAL VAL ALA SER SEQRES 7 A 160 PHE ILE GLU GLY ALA SER SER THR THR PHE CYS MSE LYS SEQRES 8 A 160 LEU GLN TYR VAL ASP GLY SER GLY THR GLN ARG TYR ASP SEQRES 9 A 160 THR ILE ASP MSE LYS THR VAL GLY PRO ASN GLN TRP VAL SEQRES 10 A 160 HIS LEU TYR ASN PRO GLN TYR ARG ILE PRO SER ASP ALA SEQRES 11 A 160 THR ASP MSE TYR VAL TYR VAL GLU THR ALA ASP ASP THR SEQRES 12 A 160 ILE ASN PHE TYR ILE ASP GLU ALA ILE GLY ALA VAL ALA SEQRES 13 A 160 GLY THR VAL ILE SEQRES 1 B 160 LYS PRO GLU GLU PRO ASP ALA GLY TYR TYR TYR HIS ASP SEQRES 2 B 160 THR PHE GLU GLY SER VAL GLY GLN TRP THR ALA ARG GLY SEQRES 3 B 160 PRO ALA GLU VAL LEU LEU SER GLY ARG THR ALA TYR LYS SEQRES 4 B 160 GLY SER GLU SER LEU LEU VAL ARG ASN ARG THR ALA ALA SEQRES 5 B 160 TRP ASN GLY ALA GLN ARG ALA LEU ASN PRO ARG THR PHE SEQRES 6 B 160 VAL PRO GLY ASN THR TYR CYS PHE SER VAL VAL ALA SER SEQRES 7 B 160 PHE ILE GLU GLY ALA SER SER THR THR PHE CYS MSE LYS SEQRES 8 B 160 LEU GLN TYR VAL ASP GLY SER GLY THR GLN ARG TYR ASP SEQRES 9 B 160 THR ILE ASP MSE LYS THR VAL GLY PRO ASN GLN TRP VAL SEQRES 10 B 160 HIS LEU TYR ASN PRO GLN TYR ARG ILE PRO SER ASP ALA SEQRES 11 B 160 THR ASP MSE TYR VAL TYR VAL GLU THR ALA ASP ASP THR SEQRES 12 B 160 ILE ASN PHE TYR ILE ASP GLU ALA ILE GLY ALA VAL ALA SEQRES 13 B 160 GLY THR VAL ILE MODRES 1DYO MSE A 90 MET SELENOMETHIONINE MODRES 1DYO MSE A 108 MET SELENOMETHIONINE MODRES 1DYO MSE A 133 MET SELENOMETHIONINE MODRES 1DYO MSE B 90 MET SELENOMETHIONINE MODRES 1DYO MSE B 108 MET SELENOMETHIONINE MODRES 1DYO MSE B 133 MET SELENOMETHIONINE HET MSE A 90 8 HET MSE A 108 8 HET MSE A 133 8 HET MSE B 90 8 HET MSE B 108 8 HET MSE B 133 8 HET CA A 300 1 HET CA B 300 1 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 3 CA 2(CA 2+) FORMUL 5 HOH *297(H2 O) SHEET 1 A 4 TYR A 9 ASP A 13 0 SHEET 2 A 4 PHE A 146 VAL A 155 -1 N GLU A 150 O ASP A 13 SHEET 3 A 4 SER A 43 ARG A 47 -1 O LEU A 44 N ILE A 148 SHEET 4 A 4 GLU A 29 SER A 33 -1 O GLU A 29 N ARG A 47 SHEET 1 A1 4 TYR A 9 ASP A 13 0 SHEET 2 A1 4 PHE A 146 VAL A 155 -1 N GLU A 150 O ASP A 13 SHEET 3 A1 4 THR A 70 SER A 78 -1 O CYS A 72 N ALA A 154 SHEET 4 A1 4 VAL A 117 ARG A 125 -1 O VAL A 117 N ALA A 77 SHEET 1 B 5 THR A 23 ARG A 25 0 SHEET 2 B 5 GLY A 55 LEU A 60 -1 O GLY A 55 N ARG A 25 SHEET 3 B 5 THR A 131 THR A 139 -1 O MSE A 133 N LEU A 60 SHEET 4 B 5 THR A 86 VAL A 95 -1 O CYS A 89 N GLU A 138 SHEET 5 B 5 GLN A 101 VAL A 111 -1 O ARG A 102 N TYR A 94 SHEET 1 C 4 TYR B 9 ASP B 13 0 SHEET 2 C 4 PHE B 146 VAL B 155 -1 N GLU B 150 O ASP B 13 SHEET 3 C 4 SER B 43 ARG B 47 -1 O LEU B 44 N ILE B 148 SHEET 4 C 4 GLU B 29 SER B 33 -1 O GLU B 29 N ARG B 47 SHEET 1 C1 4 TYR B 9 ASP B 13 0 SHEET 2 C1 4 PHE B 146 VAL B 155 -1 N GLU B 150 O ASP B 13 SHEET 3 C1 4 THR B 70 SER B 78 -1 O CYS B 72 N ALA B 154 SHEET 4 C1 4 VAL B 117 ARG B 125 -1 O VAL B 117 N ALA B 77 SHEET 1 D 5 THR B 23 ARG B 25 0 SHEET 2 D 5 GLY B 55 ALA B 59 -1 O GLY B 55 N ARG B 25 SHEET 3 D 5 THR B 131 THR B 139 -1 O VAL B 135 N ARG B 58 SHEET 4 D 5 THR B 86 VAL B 95 -1 O CYS B 89 N GLU B 138 SHEET 5 D 5 GLN B 101 VAL B 111 -1 O ARG B 102 N TYR B 94 LINK C CYS A 89 N MSE A 90 1555 1555 1.34 LINK C MSE A 90 N LYS A 91 1555 1555 1.29 LINK C ASP A 107 N MSE A 108 1555 1555 1.32 LINK C MSE A 108 N LYS A 109 1555 1555 1.33 LINK C ASP A 132 N MSE A 133 1555 1555 1.32 LINK C MSE A 133 N TYR A 134 1555 1555 1.33 LINK C CYS B 89 N MSE B 90 1555 1555 1.32 LINK C MSE B 90 N LYS B 91 1555 1555 1.33 LINK C ASP B 107 N MSE B 108 1555 1555 1.31 LINK C MSE B 108 N LYS B 109 1555 1555 1.33 LINK C ASP B 132 N MSE B 133 1555 1555 1.31 LINK C MSE B 133 N TYR B 134 1555 1555 1.30 LINK O THR A 14 CA CA A 300 1555 1555 2.46 LINK OE2 GLU A 16 CA CA A 300 1555 1555 2.87 LINK O LYS A 39 CA CA A 300 1555 1555 2.68 LINK O GLU A 42 CA CA A 300 1555 1555 2.55 LINK OD2 ASP A 149 CA CA A 300 1555 1555 3.01 LINK OD1 ASP A 149 CA CA A 300 1555 1555 2.89 LINK O THR B 14 CA CA B 300 1555 1555 2.56 LINK OE2 GLU B 16 CA CA B 300 1555 1555 2.58 LINK O LYS B 39 CA CA B 300 1555 1555 2.74 LINK O GLU B 42 CA CA B 300 1555 1555 2.56 LINK OD1 ASP B 149 CA CA B 300 1555 1555 2.69 LINK OD2 ASP B 149 CA CA B 300 1555 1555 2.71 LINK CA CA B 300 O HOH B2147 1555 1555 2.69 SITE 1 AC1 5 THR A 14 GLU A 16 LYS A 39 GLU A 42 SITE 2 AC1 5 ASP A 149 SITE 1 AC2 6 THR B 14 GLU B 16 LYS B 39 GLU B 42 SITE 2 AC2 6 ASP B 149 HOH B2147 CRYST1 89.490 89.490 207.690 90.00 90.00 120.00 P 61 2 2 24 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 0.011174 0.006451 0.000000 0.00000 SCALE2 0.000000 0.012903 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004815 0.00000 MTRIX1 1 -0.392000 0.815000 0.427000 -13.71344 1 MTRIX2 1 -0.892000 -0.450000 0.040000 69.96066 1 MTRIX3 1 0.225000 -0.366000 0.903000 39.33228 1