HEADER HYDROLASE 31-OCT-16 5H4E TITLE CRYSTAL STRUCTURE OF A BETA-1,3-GLUCANASE DOMAIN (GH64) FROM TITLE 2 CLOSTRIDIUM BEIJERINCKII COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA 1-3 GLUCANASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 215-589; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM BEIJERINCKII NCIMB 8052; SOURCE 3 ORGANISM_COMMON: CLOSTRIDIUM ACETOBUTYLICUM; SOURCE 4 ORGANISM_TAXID: 290402; SOURCE 5 STRAIN: NCIMB 8052; SOURCE 6 GENE: CBEI_2825; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HYDROLASE, BETA-1, 3-GLUCANASE EXPDTA X-RAY DIFFRACTION AUTHOR S.S.SRIVASTAVA,R.SANKARANARAYANAN REVDAT 4 08-NOV-23 5H4E 1 REMARK REVDAT 3 07-FEB-18 5H4E 1 SOURCE REVDAT 2 15-NOV-17 5H4E 1 COMPND SOURCE REMARK DBREF REVDAT 2 2 1 SEQADV SEQRES HELIX SHEET REVDAT 2 3 1 ATOM REVDAT 1 08-NOV-17 5H4E 0 JRNL AUTH S.S.SRIVASTAVA,R.SANKARANARAYANAN JRNL TITL CRYSTAL STRUCTURE OF A BETA-1,3-GLUCANASE DOMAIN (GH64) FROM JRNL TITL 2 CLOSTRIDIUM BEIJERINCKII JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 28955 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1460 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 23.6385 - 4.0071 0.99 2885 164 0.1283 0.1568 REMARK 3 2 4.0071 - 3.1831 0.99 2820 176 0.1400 0.1917 REMARK 3 3 3.1831 - 2.7814 0.98 2811 145 0.1729 0.2365 REMARK 3 4 2.7814 - 2.5274 0.97 2790 136 0.1890 0.2427 REMARK 3 5 2.5274 - 2.3464 0.97 2773 151 0.1851 0.2611 REMARK 3 6 2.3464 - 2.2082 0.96 2719 150 0.1814 0.2309 REMARK 3 7 2.2082 - 2.0977 0.95 2722 139 0.1773 0.2494 REMARK 3 8 2.0977 - 2.0064 0.95 2712 130 0.1834 0.2744 REMARK 3 9 2.0064 - 1.9292 0.94 2696 141 0.1899 0.2717 REMARK 3 10 1.9292 - 1.8627 0.90 2567 128 0.1949 0.2774 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.880 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 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 : 0.007 3061 REMARK 3 ANGLE : 1.005 4172 REMARK 3 CHIRALITY : 0.041 427 REMARK 3 PLANARITY : 0.005 547 REMARK 3 DIHEDRAL : 12.103 1056 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 5H4E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1300001998. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28957 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 40.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.22800 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3GD0 REMARK 200 REMARK 200 REMARK: DURING THE CRYSTALLIZATION PROCESS N-TERMINAL REGION GOT REMARK 200 CLEAVED. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M HEPES PH REMARK 280 7.5, 25% W/V POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K 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 36.41900 REMARK 290 SMTRY3 2 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 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: 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 328 -155.48 -146.37 REMARK 500 SER A 388 29.70 -141.24 REMARK 500 CYS A 464 -164.17 -129.03 REMARK 500 ASN A 488 16.74 -146.38 REMARK 500 ASN A 504 -157.79 -110.58 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 TYR A 490 ILE A 491 149.61 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 A1060 DISTANCE = 7.15 ANGSTROMS DBREF 5H4E A 219 593 UNP A6LX94 A6LX94_CLOB8 215 589 SEQRES 1 A 375 THR PRO PRO LEU LYS SER GLY PHE VAL THR LEU GLN VAL SEQRES 2 A 375 LYS ASN ASN THR ASN GLY GLN TYR SER ASN ASP GLN ILE SEQRES 3 A 375 TYR TRP ALA ILE VAL GLY LYS ASP PRO ASP THR LYS GLN SEQRES 4 A 375 PHE VAL HIS VAL ASP LEU ASN GLY ASN LEU ILE PRO MET SEQRES 5 A 375 LYS ILE SER ASP ASN ASP ALA ALA GLY HIS LEU THR LYS SEQRES 6 A 375 THR THR PRO ASP GLY THR PHE ASN TYR SER ASN TYR PHE SEQRES 7 A 375 CYS LYS ALA SER GLN GLN SER TYR ALA TYR ILE PRO LYS SEQRES 8 A 375 ILE ILE GLY ALA ARG MET TYR ILE SER TYR GLY LYS PRO SEQRES 9 A 375 LEU TYR ILE LYS VAL ASN GLN ALA ALA ASP GLY LEU ILE SEQRES 10 A 375 GLY TYR ALA GLY PRO ASN LEU ALA ASN THR SER ASP PRO SEQRES 11 A 375 ASN THR GLY ILE MET PHE GLU TRP ALA GLU MET ALA TRP SEQRES 12 A 375 THR ASN ASP GLY LEU TRP ILE ASN THR THR ARG VAL ASP SEQRES 13 A 375 GLN PHE CYS TYR PRO TYR ASN ILE GLN LEU VAL GLY ASN SEQRES 14 A 375 SER GLY TYR ASN LYS THR TYR GLY ASP THR GLY THR ARG SEQRES 15 A 375 ALA ASP LEU MET ASN ALA TYR LYS ASN SER VAL PRO ALA SEQRES 16 A 375 GLU PHE LYS SER LEU VAL HIS SER ASP ARG ILE TYR ALA SEQRES 17 A 375 PRO ALA SER GLY LEU GLY THR PHE THR ALA SER GLN ALA SEQRES 18 A 375 ASN ALA HIS TYR PHE ASP SER TYR ILE ASN ASP VAL TYR SEQRES 19 A 375 SER TYR TYR ALA THR HIS GLU LEU THR PHE THR CYS ASP SEQRES 20 A 375 ARG GLY THR TYR SER GLY HIS VAL VAL GLY ASN ASP PHE SEQRES 21 A 375 VAL PHE ASN LYS ASN GLY GLY ALA TYR ASN LEU TYR ILE SEQRES 22 A 375 HIS GLY LYS PRO SER THR GLN GLU VAL LEU LEU GLY ASN SEQRES 23 A 375 GLY ILE PHE ASP GLY GLY ASN ASP ASP GLU LYS ALA ILE SEQRES 24 A 375 LYS ALA GLN VAL CYS ALA ALA PHE ASN ARG HIS VAL MET SEQRES 25 A 375 LEU ASP PRO ALA HIS TRP ASN ASN SER ALA TYR PHE TYR SEQRES 26 A 375 LYS ASP ALA PRO ALA ASN TYR PHE ALA LYS PHE TRP HIS SEQRES 27 A 375 ASP HIS SER TYR GLU ASN LYS SER TYR GLY PHE CYS TYR SEQRES 28 A 375 ASP ASP VAL PHE ASP PHE SER SER THR LEU HIS VAL ALA SEQRES 29 A 375 ASP PRO LYS TYR ALA ILE ILE ASN VAL GLY TRP FORMUL 2 HOH *460(H2 O) HELIX 1 AA1 SER A 240 ASP A 242 5 3 HELIX 2 AA2 LYS A 271 ASP A 276 5 6 HELIX 3 AA3 THR A 399 VAL A 411 1 13 HELIX 4 AA4 PRO A 412 SER A 417 1 6 HELIX 5 AA5 PHE A 444 TYR A 455 1 12 HELIX 6 AA6 SER A 496 GLY A 503 1 8 HELIX 7 AA7 ASN A 504 ASP A 508 5 5 HELIX 8 AA8 ASN A 511 ARG A 527 1 17 HELIX 9 AA9 ASP A 532 TRP A 536 5 5 HELIX 10 AB1 ASN A 538 PHE A 542 5 5 HELIX 11 AB2 ASN A 549 HIS A 558 1 10 HELIX 12 AB3 SER A 559 LYS A 563 5 5 HELIX 13 AB4 ASP A 571 PHE A 575 5 5 SHEET 1 AA1 5 TYR A 304 ILE A 307 0 SHEET 2 AA1 5 VAL A 227 ASN A 234 -1 N LEU A 229 O ALA A 305 SHEET 3 AA1 5 PRO A 584 GLY A 592 1 O ILE A 589 N GLN A 230 SHEET 4 AA1 5 TYR A 380 GLY A 386 -1 N VAL A 385 O TYR A 586 SHEET 5 AA1 5 ASN A 391 GLY A 395 -1 O LYS A 392 N LEU A 384 SHEET 1 AA2 4 LEU A 267 PRO A 269 0 SHEET 2 AA2 4 PHE A 258 VAL A 261 -1 N HIS A 260 O ILE A 268 SHEET 3 AA2 4 ILE A 244 LYS A 251 -1 N GLY A 250 O VAL A 259 SHEET 4 AA2 4 CYS A 297 LYS A 298 -1 O CYS A 297 N TRP A 246 SHEET 1 AA3 7 LEU A 267 PRO A 269 0 SHEET 2 AA3 7 PHE A 258 VAL A 261 -1 N HIS A 260 O ILE A 268 SHEET 3 AA3 7 ILE A 244 LYS A 251 -1 N GLY A 250 O VAL A 259 SHEET 4 AA3 7 ILE A 310 TYR A 319 -1 O ARG A 314 N VAL A 249 SHEET 5 AA3 7 PHE A 354 THR A 362 -1 O TRP A 361 N ILE A 310 SHEET 6 AA3 7 GLY A 365 ASN A 369 -1 O ASN A 369 N GLU A 358 SHEET 7 AA3 7 LEU A 579 VAL A 581 -1 O LEU A 579 N ILE A 368 SHEET 1 AA4 2 LEU A 281 THR A 285 0 SHEET 2 AA4 2 GLY A 288 TYR A 292 -1 O GLY A 288 N THR A 285 SHEET 1 AA5 2 LYS A 326 GLN A 329 0 SHEET 2 AA5 2 ILE A 335 ALA A 338 -1 O GLY A 336 N ASN A 328 SHEET 1 AA6 2 GLN A 375 PHE A 376 0 SHEET 2 AA6 2 ILE A 424 TYR A 425 -1 O ILE A 424 N PHE A 376 SHEET 1 AA7 4 LEU A 460 CYS A 464 0 SHEET 2 AA7 4 GLY A 467 VAL A 474 -1 O GLY A 471 N LEU A 460 SHEET 3 AA7 4 ASP A 477 LYS A 482 -1 O VAL A 479 N HIS A 472 SHEET 4 AA7 4 LEU A 489 ILE A 491 -1 O LEU A 489 N PHE A 480 CISPEP 1 ALA A 546 PRO A 547 0 -0.22 CRYST1 45.758 72.838 56.456 90.00 103.85 90.00 P 1 21 1 2 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 0.021854 0.000000 0.005386 0.00000 SCALE2 0.000000 0.013729 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018243 0.00000