HEADER HYDROLASE 25-SEP-19 6UFV TITLE CRYSTAL STRUCTURE OF THE CBM3 FROM BACILLUS SUBTILIS AT 1.06 ANGSTROM TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOGLUCANASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CARBOXYMETHYL-CELLULASE,CELLULASE,ENDO-1,4-BETA-GLUCANASE; COMPND 5 EC: 3.2.1.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS (STRAIN 168); SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: EGLS, BGLC, GLD, BSU18130; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CARBOHYDRATE-BINDING MODULE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.A.B.MORAIS,J.H.PAIVA,M.T.MURAKAMI REVDAT 1 30-SEP-20 6UFV 0 JRNL AUTH M.A.B.MORAIS,J.H.PAIVA,M.T.MURAKAMI JRNL TITL CRYSTAL STRUCTURE OF THE CBM3 FROM BACILLUS SUBTILIS AT 1.06 JRNL TITL 2 ANGSTROM RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 76883 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3919 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 3.2155 - 2.5536 1.00 2731 140 0.1756 0.1837 REMARK 3 2 2.5536 - 2.2312 1.00 2715 119 0.1716 0.1698 REMARK 3 3 2.2312 - 2.0274 1.00 2689 163 0.1430 0.1517 REMARK 3 4 2.0274 - 1.8822 1.00 2680 132 0.1369 0.1587 REMARK 3 5 1.8822 - 1.7713 1.00 2656 143 0.1417 0.1684 REMARK 3 6 1.7713 - 1.6826 1.00 2676 122 0.1376 0.1697 REMARK 3 7 1.6826 - 1.6094 1.00 2648 148 0.1319 0.1478 REMARK 3 8 1.6094 - 1.5474 1.00 2639 145 0.1291 0.1511 REMARK 3 9 1.5474 - 1.4940 0.99 2620 136 0.1283 0.1883 REMARK 3 10 1.4940 - 1.4473 1.00 2611 153 0.1310 0.1788 REMARK 3 11 1.4473 - 1.4060 1.00 2645 144 0.1357 0.1555 REMARK 3 12 1.4060 - 1.3690 0.99 2635 143 0.1395 0.1822 REMARK 3 13 1.3690 - 1.3356 0.99 2594 148 0.1488 0.1761 REMARK 3 14 1.3356 - 1.3052 0.99 2609 135 0.1527 0.1857 REMARK 3 15 1.3052 - 1.2774 0.99 2608 130 0.1630 0.2034 REMARK 3 16 1.2774 - 1.2519 0.99 2580 152 0.1693 0.1700 REMARK 3 17 1.2519 - 1.2283 0.98 2595 121 0.1794 0.1939 REMARK 3 18 1.2283 - 1.2063 0.99 2619 124 0.2077 0.2575 REMARK 3 19 1.2063 - 1.1859 0.99 2590 142 0.2017 0.2467 REMARK 3 20 1.1859 - 1.1668 0.98 2590 147 0.2137 0.2689 REMARK 3 21 1.1668 - 1.1488 0.98 2557 143 0.2123 0.2394 REMARK 3 22 1.1488 - 1.1319 0.98 2540 147 0.2196 0.2701 REMARK 3 23 1.1319 - 1.1160 0.97 2497 171 0.2578 0.2883 REMARK 3 24 1.1160 - 1.1009 0.97 2558 132 0.2922 0.2992 REMARK 3 25 1.1009 - 1.0866 0.97 2536 160 0.3339 0.3776 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.47 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 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 : 0.016 1227 REMARK 3 ANGLE : 1.666 1657 REMARK 3 CHIRALITY : 0.087 172 REMARK 3 PLANARITY : 0.010 218 REMARK 3 DIHEDRAL : 13.625 449 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 6UFV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1000232753. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77710 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.060 REMARK 200 RESOLUTION RANGE LOW (A) : 21.305 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 51.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 % (W/V) PEG 3350, 0.20 M POTASSIUM REMARK 280 THIOCYNATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.07650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.32600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.72400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.32600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.07650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.72400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 A 829 DISTANCE = 5.82 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 501 DBREF 6UFV A 354 499 UNP P10475 GUN2_BACSU 354 499 SEQADV 6UFV MET A 351 UNP P10475 INITIATING METHIONINE SEQADV 6UFV ALA A 352 UNP P10475 EXPRESSION TAG SEQADV 6UFV SER A 353 UNP P10475 EXPRESSION TAG SEQRES 1 A 149 MET ALA SER ILE SER VAL GLN TYR ARG ALA GLY ASP GLY SEQRES 2 A 149 SER MET ASN SER ASN GLN ILE ARG PRO GLN LEU GLN ILE SEQRES 3 A 149 LYS ASN ASN GLY ASN THR THR VAL ASP LEU LYS ASP VAL SEQRES 4 A 149 THR ALA ARG TYR TRP TYR LYS ALA LYS ASN LYS GLY GLN SEQRES 5 A 149 ASN PHE ASP CYS ASP TYR ALA GLN ILE GLY CYS GLY ASN SEQRES 6 A 149 VAL THR HIS LYS PHE VAL THR LEU HIS LYS PRO LYS GLN SEQRES 7 A 149 GLY ALA ASP THR TYR LEU GLU LEU GLY PHE LYS ASN GLY SEQRES 8 A 149 THR LEU ALA PRO GLY ALA SER THR GLY ASN ILE GLN LEU SEQRES 9 A 149 ARG LEU HIS ASN ASP ASP TRP SER ASN TYR ALA GLN SER SEQRES 10 A 149 GLY ASP TYR SER PHE PHE LYS SER ASN THR PHE LYS THR SEQRES 11 A 149 THR LYS LYS ILE THR LEU TYR ASP GLN GLY LYS LEU ILE SEQRES 12 A 149 TRP GLY THR GLU PRO ASN HET PEG A 501 7 HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 PEG C4 H10 O3 FORMUL 3 HOH *229(H2 O) HELIX 1 AA1 GLY A 412 GLY A 414 5 3 HELIX 2 AA2 ALA A 465 ASP A 469 5 5 SHEET 1 AA1 5 GLN A 402 ALA A 409 0 SHEET 2 AA1 5 ILE A 452 ASN A 458 -1 O GLN A 453 N TYR A 408 SHEET 3 AA1 5 PRO A 372 ASN A 378 -1 N PRO A 372 O LEU A 454 SHEET 4 AA1 5 ILE A 354 ALA A 360 -1 N SER A 355 O LYS A 377 SHEET 5 AA1 5 LYS A 479 THR A 480 -1 O LYS A 479 N TYR A 358 SHEET 1 AA2 2 VAL A 384 ASP A 385 0 SHEET 2 AA2 2 THR A 442 LEU A 443 -1 O LEU A 443 N VAL A 384 SHEET 1 AA3 5 VAL A 416 LYS A 427 0 SHEET 2 AA3 5 ALA A 430 PHE A 438 -1 O ALA A 430 N LYS A 427 SHEET 3 AA3 5 VAL A 389 TYR A 395 -1 N ALA A 391 O LEU A 436 SHEET 4 AA3 5 ILE A 484 ASP A 488 -1 O THR A 485 N ARG A 392 SHEET 5 AA3 5 LYS A 491 TRP A 494 -1 O ILE A 493 N LEU A 486 SSBOND 1 CYS A 406 CYS A 413 1555 1555 2.08 SITE 1 AC1 8 MET A 351 ALA A 352 ASP A 460 TRP A 461 SITE 2 AC1 8 SER A 462 ASN A 463 ILE A 493 HOH A 614 CRYST1 46.153 55.448 66.652 90.00 90.00 90.00 P 21 21 21 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 0.021667 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018035 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015003 0.00000