PDB Short entry for 1DAQ HEADER HYDROLASE 31-OCT-99 1DAQ TITLE SOLUTION STRUCTURE OF THE TYPE I DOCKERIN DOMAIN FROM THE CLOSTRIDIUM TITLE 2 THERMOCELLUM CELLULOSOME (MINIMIZED AVERAGE STRUCTURE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOGLUCANASE SS; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TYPE I DOCKERIN DOMAIN (RESIDUES 673-741); COMPND 5 SYNONYM: CELS; COMPND 6 EC: 3.2.1.4; COMPND 7 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; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: JM109(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PCYB2 KEYWDS CELLULOSE DEGRADATION, CELLULOSOME, CALCIUM-BINDING, HYDROLASE EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR B.L.LYTLE,B.F.VOLKMAN,W.M.WESTLER,M.P.HECKMAN,J.H.D.WU REVDAT 4 03-NOV-21 1DAQ 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1DAQ 1 VERSN REVDAT 2 01-APR-03 1DAQ 1 JRNL REVDAT 1 04-APR-01 1DAQ 0 JRNL AUTH B.L.LYTLE,B.F.VOLKMAN,W.M.WESTLER,M.P.HECKMAN,J.H.WU JRNL TITL SOLUTION STRUCTURE OF A TYPE I DOCKERIN DOMAIN, A NOVEL JRNL TITL 2 PROKARYOTIC, EXTRACELLULAR CALCIUM-BINDING DOMAIN. JRNL REF J.MOL.BIOL. V. 307 745 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11273698 JRNL DOI 10.1006/JMBI.2001.4522 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.L.LYTLE,B.F.VOLKMAN,W.M.WESTLER,J.H.D.WU REMARK 1 TITL SECONDARY STRUCTURE AND CALCIUM-INDUCED FOLDING OF THE REMARK 1 TITL 2 CLOSTRIDIUM THERMOCELLUM DOCKERIN DOMAIN DETERMINED BY NMR REMARK 1 TITL 3 SPECTROSCOPY REMARK 1 REF ARCH.BIOCHEM.BIOPHYS. V. 379 237 2000 REMARK 1 REFN ISSN 0003-9861 REMARK 1 DOI 10.1006/ABBI.2000.1882 REMARK 1 REFERENCE 2 REMARK 1 AUTH B.LYTLE,J.H.D.WU REMARK 1 TITL INVOLVEMENT OF BOTH DOCKERIN SUBDOMAINS IN ASSEMBLY OF THE REMARK 1 TITL 2 CLOSTRIDIUM THERMOCELLUM CELLULOSOME REMARK 1 REF J.BACTERIOL. V. 180 6581 1998 REMARK 1 REFN ISSN 0021-9193 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5 REMARK 3 AUTHORS : P.GUENTERT, C.MUMENTHALER, K.WUETHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON 728 NOE REMARK 3 -DERIVED DISTANCE CONSTRAINTS, 79 DIHEDRAL ANGLE CONSTRAINTS, REMARK 3 AND 12 CALCIUM ION RESTRAINTS. REMARK 4 REMARK 4 1DAQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-NOV-99. REMARK 100 THE DEPOSITION ID IS D_1000009931. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 328; 328 REMARK 210 PH : 6.0; 6.0 REMARK 210 IONIC STRENGTH : 100MM KCL; 100MM KCL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 100MM POTASSIUM CHLORIDE; 20MM REMARK 210 CALCIUM CHLORIDE; 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 2D REMARK 210 NOESY; 3D_15N-SEPARATED_TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA 1.5, FELIX 95.0, NMRPIPE, REMARK 210 XEASY 1.2 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED BY STANDARD TECHNIQUES USING REMARK 210 UNLABELED AND 15N- LABELED DOCKERIN. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 LEU A 23 H VAL A 27 1.51 REMARK 500 O LEU A 55 H ILE A 59 1.52 REMARK 500 O ASP A 8 HD21 ASN A 35 1.59 REMARK 500 OD1 ASN A 16 H THR A 18 1.60 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 LEU A 5 148.17 -170.00 REMARK 500 ARG A 29 -179.44 -179.59 REMARK 500 LEU A 41 19.36 -148.17 REMARK 500 ASN A 42 20.96 -153.51 REMARK 500 ARG A 46 -93.47 -145.88 REMARK 500 SER A 49 -30.74 166.61 REMARK 500 LYS A 61 -36.57 -177.07 REMARK 500 ILE A 63 99.21 -33.20 REMARK 500 ASP A 64 -34.63 174.65 REMARK 500 THR A 65 -41.97 -130.70 REMARK 500 LEU A 66 94.88 67.91 REMARK 500 TYR A 68 117.99 -38.17 REMARK 500 REMARK 500 REMARK: NULL 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 72 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 8 OD1 REMARK 620 2 ASN A 10 OD1 75.7 REMARK 620 3 ASP A 12 OD2 108.7 106.2 REMARK 620 4 LYS A 14 O 70.9 126.1 123.9 REMARK 620 5 ASP A 19 OD1 121.5 71.0 126.0 92.1 REMARK 620 6 ASP A 19 OD2 84.2 85.0 164.5 51.0 46.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 73 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 40 OD1 REMARK 620 2 LEU A 41 N 52.3 REMARK 620 3 ASN A 42 OD1 87.2 66.4 REMARK 620 4 ASP A 44 OD2 83.9 121.6 76.2 REMARK 620 5 ARG A 46 O 122.4 121.3 148.5 114.2 REMARK 620 6 ASP A 51 OD1 131.5 115.6 52.3 63.4 104.0 REMARK 620 7 ASP A 51 OD2 134.7 84.5 60.3 114.1 89.1 51.1 REMARK 620 N 1 2 3 4 5 6 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR-DETERMINED REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: I REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: FIRST PREDICTED CA2+ BINDING LOOP REMARK 800 REMARK 800 SITE_IDENTIFIER: II REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: SECOND PREDICTED CA2+ BINDING LOOP REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 72 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 73 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DAV RELATED DB: PDB REMARK 900 NMR, 20 STRUCTURES DBREF 1DAQ A 1 70 UNP P38686 GUNS_CLOTM 672 741 SEQADV 1DAQ MET A 1 UNP P38686 PRO 672 ENGINEERED MUTATION SEQADV 1DAQ GLY A 71 UNP P38686 ENGINEERED MUTATION SEQRES 1 A 71 MET SER THR LYS LEU TYR GLY ASP VAL ASN ASP ASP GLY SEQRES 2 A 71 LYS VAL ASN SER THR ASP ALA VAL ALA LEU LYS ARG TYR SEQRES 3 A 71 VAL LEU ARG SER GLY ILE SER ILE ASN THR ASP ASN ALA SEQRES 4 A 71 ASP LEU ASN GLU ASP GLY ARG VAL ASN SER THR ASP LEU SEQRES 5 A 71 GLY ILE LEU LYS ARG TYR ILE LEU LYS GLU ILE ASP THR SEQRES 6 A 71 LEU PRO TYR LYS ASN GLY HET CA A 72 1 HET CA A 73 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 1 ASP A 19 ARG A 29 1 11 HELIX 2 2 THR A 36 ALA A 39 5 4 HELIX 3 3 ASP A 51 ILE A 59 1 9 LINK OD1 ASP A 8 CA CA A 72 1555 1555 3.00 LINK OD1 ASN A 10 CA CA A 72 1555 1555 2.80 LINK OD2 ASP A 12 CA CA A 72 1555 1555 2.82 LINK O LYS A 14 CA CA A 72 1555 1555 2.73 LINK OD1 ASP A 19 CA CA A 72 1555 1555 2.78 LINK OD2 ASP A 19 CA CA A 72 1555 1555 2.82 LINK OD1 ASP A 40 CA CA A 73 1555 1555 3.06 LINK N LEU A 41 CA CA A 73 1555 1555 3.19 LINK OD1 ASN A 42 CA CA A 73 1555 1555 2.56 LINK OD2 ASP A 44 CA CA A 73 1555 1555 2.77 LINK O ARG A 46 CA CA A 73 1555 1555 2.85 LINK OD1 ASP A 51 CA CA A 73 1555 1555 2.83 LINK OD2 ASP A 51 CA CA A 73 1555 1555 2.12 SITE 1 I 12 ASP A 8 VAL A 9 ASN A 10 ASP A 11 SITE 2 I 12 ASP A 12 GLY A 13 LYS A 14 VAL A 15 SITE 3 I 12 ASN A 16 SER A 17 THR A 18 ASP A 19 SITE 1 II 12 ASP A 40 LEU A 41 ASN A 42 GLU A 43 SITE 2 II 12 ASP A 44 GLY A 45 ARG A 46 VAL A 47 SITE 3 II 12 ASN A 48 SER A 49 THR A 50 ASP A 51 SITE 1 AC1 6 ASP A 8 ASN A 10 ASP A 12 GLY A 13 SITE 2 AC1 6 LYS A 14 ASP A 19 SITE 1 AC2 6 ASP A 40 LEU A 41 ASN A 42 ASP A 44 SITE 2 AC2 6 ARG A 46 ASP A 51 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000