HEADER CARBOHYDRATE-BINDING PROTEIN 04-SEP-12 4B9C TITLE BIOMASS SENSORING MODULES FROM PUTATIVE RSGI-LIKE PROTEINS OF TITLE 2 CLOSTRIDIUM THERMOCELLUM RESEMBLE FAMILY 3 CARBOHYDRATE-BINDING TITLE 3 MODULE OF CELLULOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE 3A CELLULOSE-BINDING DOMAIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FAMILY 3B CARBOHYDRATE BINDING MODULE, RESIDUES 340-485; COMPND 5 SYNONYM: RSGI1 PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM THERMOCELLUM; SOURCE 3 ORGANISM_TAXID: 203119; SOURCE 4 ATCC: 27405; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS CARBOHYDRATE-BINDING PROTEIN, BIOMASS SENSORING SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR O.YANIV,L.J.W.SHIMON,E.A.BAYER,R.LAMED,F.FROLOW REVDAT 4 20-DEC-23 4B9C 1 REMARK LINK REVDAT 3 26-FEB-14 4B9C 1 JRNL REVDAT 2 12-FEB-14 4B9C 1 JRNL REVDAT 1 11-SEP-13 4B9C 0 JRNL AUTH O.YANIV,G.FICHMAN,I.BOROVOK,Y.SHOHAM,E.A.BAYER,R.LAMED, JRNL AUTH 2 L.J.W.SHIMON,F.FROLOW JRNL TITL FINE-STRUCTURAL VARIANCE OF FAMILY 3 CARBOHYDRATE-BINDING JRNL TITL 2 MODULES AS EXTRACELLULAR BIOMASS-SENSING COMPONENTS OF JRNL TITL 3 CLOSTRIDIUM THERMOCELLUM ANTI-SIGMA(I) FACTORS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 522 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24531486 JRNL DOI 10.1107/S139900471302926X REMARK 2 REMARK 2 RESOLUTION. 1.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 50.7 REMARK 3 NUMBER OF REFLECTIONS : 48184 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2441 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.2059 - 3.0103 0.68 3560 202 0.1662 0.1917 REMARK 3 2 3.0103 - 2.3895 0.83 4424 224 0.1796 0.1872 REMARK 3 3 2.3895 - 2.0875 0.85 4531 200 0.1688 0.1703 REMARK 3 4 2.0875 - 1.8966 0.83 4403 251 0.1553 0.1973 REMARK 3 5 1.8966 - 1.7607 0.90 4836 245 0.1568 0.1584 REMARK 3 6 1.7607 - 1.6569 0.70 3694 178 0.1682 0.1767 REMARK 3 7 1.6569 - 1.5739 0.65 3456 174 0.1686 0.1760 REMARK 3 8 1.5739 - 1.5054 0.55 2902 169 0.1829 0.1736 REMARK 3 9 1.5054 - 1.4474 0.50 2658 154 0.1887 0.2105 REMARK 3 10 1.4474 - 1.3975 0.47 2453 142 0.1879 0.2036 REMARK 3 11 1.3975 - 1.3538 0.43 2269 136 0.2001 0.1956 REMARK 3 12 1.3538 - 1.3151 0.39 2066 111 0.1970 0.1980 REMARK 3 13 1.3151 - 1.2804 0.30 1621 78 0.2018 0.2240 REMARK 3 14 1.2804 - 1.2492 0.22 1180 71 0.2003 0.2223 REMARK 3 15 1.2492 - 1.2208 0.15 786 42 0.2163 0.1825 REMARK 3 16 1.2208 - 1.1948 0.10 534 30 0.1807 0.1657 REMARK 3 17 1.1948 - 1.1709 0.07 370 34 0.1779 0.1785 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 1.51 REMARK 3 B_SOL : 0.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.61210 REMARK 3 B22 (A**2) : 0.55230 REMARK 3 B33 (A**2) : -0.16380 REMARK 3 B12 (A**2) : 0.17790 REMARK 3 B13 (A**2) : -0.12870 REMARK 3 B23 (A**2) : -0.82480 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1313 REMARK 3 ANGLE : 1.157 1773 REMARK 3 CHIRALITY : 0.096 171 REMARK 3 PLANARITY : 0.006 228 REMARK 3 DIHEDRAL : 13.612 487 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4B9C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1290053960. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : LIQUID NITROGEN COOLED CHANNEL REMARK 200 -CUT SILICON MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48184 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.170 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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 4B97 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM MALONATE PH 4.0 20 % PEG REMARK 280 3350, PH 5.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 47.41750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.70875 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 71.12625 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 A 2061 O HOH A 2064 2.13 REMARK 500 O HOH A 2020 O HOH A 2021 2.19 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 SER A 2 39.61 -150.72 REMARK 500 ASN A 99 -0.68 73.86 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 A1151 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 47 O REMARK 620 2 GLU A 117 O 172.3 REMARK 620 3 ASP A 120 OD1 112.8 74.1 REMARK 620 4 ASP A 121 OD1 85.6 93.4 73.4 REMARK 620 5 HOH A2072 O 85.0 87.3 141.9 74.8 REMARK 620 6 HOH A2073 O 94.6 82.2 133.9 148.1 73.5 REMARK 620 7 HOH A2074 O 82.2 103.2 77.5 140.9 140.1 70.2 REMARK 620 N 1 2 3 4 5 6 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 1151 DBREF 4B9C A 5 150 UNP A3DBH1 A3DBH1_CLOTH 340 485 SEQADV 4B9C GLY A 1 UNP A3DBH1 EXPRESSION TAG SEQADV 4B9C SER A 2 UNP A3DBH1 EXPRESSION TAG SEQADV 4B9C HIS A 3 UNP A3DBH1 EXPRESSION TAG SEQADV 4B9C MET A 4 UNP A3DBH1 EXPRESSION TAG SEQRES 1 A 150 GLY SER HIS MET GLY LEU LYS ILE GLN TYR TYR SER ARG SEQRES 2 A 150 LYS PRO HIS ASP SER ALA GLY ILE ASP PHE SER PHE ARG SEQRES 3 A 150 MET PHE ASN THR GLY ASN GLU ALA ILE ASP LEU LYS ASP SEQRES 4 A 150 VAL LYS VAL ARG TYR TYR PHE LYS GLU ASP VAL SER ILE SEQRES 5 A 150 ASP GLU MET ASN TRP ALA VAL TYR PHE TYR SER LEU GLY SEQRES 6 A 150 SER GLU LYS ASP VAL GLN CYS ARG PHE TYR GLU LEU PRO SEQRES 7 A 150 GLY LYS LYS GLU ALA ASN LYS TYR LEU GLU ILE THR PHE SEQRES 8 A 150 LYS SER GLY THR LEU SER PRO ASN ASP VAL MET TYR ILE SEQRES 9 A 150 THR GLY GLU PHE TYR LYS ASN ASP TRP THR LYS PHE GLU SEQRES 10 A 150 GLN ARG ASP ASP TYR SER TYR ASN PRO ALA ASP SER TYR SEQRES 11 A 150 SER ASP TRP LYS ARG MET THR ALA TYR ILE SER ASN LYS SEQRES 12 A 150 LEU VAL TRP GLY ILE GLU PRO HET CA A1151 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *167(H2 O) HELIX 1 1 SER A 51 ASP A 53 5 3 HELIX 2 2 SER A 66 LYS A 68 5 3 SHEET 1 AA 4 LEU A 6 GLN A 9 0 SHEET 2 AA 4 PHE A 25 ASN A 29 -1 O ARG A 26 N GLN A 9 SHEET 3 AA 4 VAL A 101 LYS A 110 -1 O MET A 102 N MET A 27 SHEET 4 AA 4 MET A 55 TYR A 62 -1 O ASN A 56 N TYR A 109 SHEET 1 AB 4 LEU A 6 GLN A 9 0 SHEET 2 AB 4 PHE A 25 ASN A 29 -1 O ARG A 26 N GLN A 9 SHEET 3 AB 4 VAL A 101 LYS A 110 -1 O MET A 102 N MET A 27 SHEET 4 AB 4 GLY A 20 ASP A 22 1 O ILE A 21 N PHE A 108 SHEET 1 AC 2 MET A 55 TYR A 62 0 SHEET 2 AC 2 VAL A 101 LYS A 110 -1 O THR A 105 N TYR A 60 SHEET 1 AD 2 ASP A 17 SER A 18 0 SHEET 2 AD 2 PHE A 116 GLU A 117 -1 O PHE A 116 N SER A 18 SHEET 1 AE 2 ILE A 35 ASP A 36 0 SHEET 2 AE 2 THR A 95 LEU A 96 -1 O LEU A 96 N ILE A 35 SHEET 1 AF 5 VAL A 70 GLU A 76 0 SHEET 2 AF 5 LYS A 85 PHE A 91 -1 O TYR A 86 N TYR A 75 SHEET 3 AF 5 VAL A 40 PHE A 46 -1 O VAL A 40 N PHE A 91 SHEET 4 AF 5 MET A 136 ILE A 140 -1 O THR A 137 N ARG A 43 SHEET 5 AF 5 LYS A 143 TRP A 146 -1 O LYS A 143 N ILE A 140 LINK O LYS A 47 CA CA A1151 1555 1555 2.35 LINK O GLU A 117 CA CA A1151 1555 1555 2.33 LINK OD1 ASP A 120 CA CA A1151 1555 1555 2.48 LINK OD1 ASP A 121 CA CA A1151 1555 1555 2.51 LINK CA CA A1151 O HOH A2072 1555 1555 2.37 LINK CA CA A1151 O HOH A2073 1555 1555 2.56 LINK CA CA A1151 O HOH A2074 1555 1555 2.36 SITE 1 AC1 7 LYS A 47 GLU A 117 ASP A 120 ASP A 121 SITE 2 AC1 7 HOH A2072 HOH A2073 HOH A2074 CRYST1 39.184 39.184 94.835 90.00 90.00 90.00 P 41 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 0.025521 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025521 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010545 0.00000