HEADER HYDROLASE 21-MAY-13 4BOK TITLE CRYSTAL STRUCTURE OF BACILLUS CIRCULANS TN-31 AMAN6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-1,6-MANNANASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 35-375; COMPND 5 SYNONYM: AMAN6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CIRCULANS; SOURCE 3 ORGANISM_TAXID: 1397; SOURCE 4 STRAIN: TN-31; SOURCE 5 ATCC: 29101; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.STRIEBECK,D.M.F.VAN AALTEN REVDAT 1 28-MAY-14 4BOK 0 JRNL AUTH A.STRIEBECK,V.S.BORODKIN,A.T.FERENBACH,D.M.F.VAN AALTEN JRNL TITL THE STRUCTURE OF B. CIRCULANS AMAN6 DEFINES THE FOLD AND JRNL TITL 2 MECHANISM OF THE GH-76 MANNOPROTEIN TRANSGLYCOSYLASES AND JRNL TITL 3 BACTERIAL MANNOSIDASES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 2.047 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.120 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.36 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.71 REMARK 3 NUMBER OF REFLECTIONS : 19461 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1727 REMARK 3 R VALUE (WORKING SET) : 0.1702 REMARK 3 FREE R VALUE : 0.2121 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 997 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 40.1278 - 3.9155 1.00 2799 145 0.1583 0.1793 REMARK 3 2 3.9155 - 3.1082 1.00 2657 152 0.1475 0.1755 REMARK 3 3 3.1082 - 2.7154 1.00 2637 143 0.1780 0.2208 REMARK 3 4 2.7154 - 2.4672 1.00 2629 149 0.1757 0.2612 REMARK 3 5 2.4672 - 2.2904 1.00 2608 137 0.1775 0.2224 REMARK 3 6 2.2904 - 2.1553 1.00 2603 119 0.1979 0.2788 REMARK 3 7 2.1553 - 2.0474 0.98 2531 152 0.2138 0.2622 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.06 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.91 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.11 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 : 0.003 2805 REMARK 3 ANGLE : 0.679 3818 REMARK 3 CHIRALITY : 0.053 387 REMARK 3 PLANARITY : 0.003 499 REMARK 3 DIHEDRAL : 14.482 965 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 4BOK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAY-13. REMARK 100 THE PDBE ID CODE IS EBI-56920. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.969 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19462 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.00 REMARK 200 RESOLUTION RANGE LOW (A) : 40.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.2 REMARK 200 R MERGE (I) : 0.12 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.80 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 11.8 REMARK 200 R MERGE FOR SHELL (I) : 0.45 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.10 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 25.47400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.12100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.54650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.12100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.47400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.54650 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 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 ILE A 375 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 176 CG REMARK 480 GLU A 233 CD REMARK 480 GLU A 321 CD 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 279 36.80 -92.93 REMARK 500 HIS A 345 47.77 -90.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BOJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACILLUS CIRCULANS TN-31 AMAN6 IN REMARK 900 COMPLEX WITH MANNOBIOSE DBREF 4BOK A 35 375 UNP Q9Z4P9 Q9Z4P9_BACCI 35 375 SEQRES 1 A 341 ALA TYR THR ALA SER ASP GLY ASP THR ALA MET LYS ALA SEQRES 2 A 341 PHE ASN ASP THR PHE TRP ASP PRO ASN ALA LYS MET PHE SEQRES 3 A 341 TRP LYS ASP SER LYS ARG GLU LYS HIS GLN ASP PHE TRP SEQRES 4 A 341 VAL GLU ALA GLU LEU TRP GLU LEU VAL MET ASP ALA TYR SEQRES 5 A 341 GLN HIS THR SER ASP PRO ALA LEU LYS ALA GLU LEU LYS SEQRES 6 A 341 THR GLN ILE ASP ASP VAL TYR ASP GLY THR VAL ALA LYS SEQRES 7 A 341 TYR GLY GLN ASP TRP THR ASN ASN PRO PHE ASN ASP ASP SEQRES 8 A 341 ILE MET TRP TRP ALA MET GLY SER ALA ARG ALA TYR GLN SEQRES 9 A 341 ILE THR GLY ASN PRO ARG TYR LEU GLU ALA ALA ARG ASP SEQRES 10 A 341 HIS PHE ASP PHE VAL TYR ASP THR GLN TRP ASP GLU GLU SEQRES 11 A 341 PHE ALA ASN GLY GLY ILE TRP TRP LEU ASN SER ASP HIS SEQRES 12 A 341 ASN THR LYS ASN ALA CYS ILE ASN PHE PRO ALA ALA GLN SEQRES 13 A 341 ALA ALA LEU TYR LEU TYR ASP ILE THR LYS ASP GLU HIS SEQRES 14 A 341 TYR LEU ASN ALA ALA THR LYS ILE PHE ARG TRP GLY LYS SEQRES 15 A 341 THR MET LEU THR ASP GLY ASN GLY LYS VAL PHE ASP ARG SEQRES 16 A 341 ILE GLU ILE GLU HIS GLY ALA VAL PRO ASP ALA THR HIS SEQRES 17 A 341 TYR ASN GLN GLY THR TYR ILE GLY SER ALA VAL GLY LEU SEQRES 18 A 341 TYR LYS ALA THR GLY ASN ALA VAL TYR LEU ASP ASP ALA SEQRES 19 A 341 VAL LYS ALA ALA LYS PHE THR LYS ASN HIS LEU VAL ASP SEQRES 20 A 341 SER ASN GLY VAL LEU ASN TYR GLU GLY PRO ASN GLY ASP SEQRES 21 A 341 LEU LYS GLY GLY LYS THR ILE LEU MET ARG ASN LEU ALA SEQRES 22 A 341 HIS LEU GLN LYS THR LEU ASP GLU THR GLY GLN TYR PRO SEQRES 23 A 341 GLU PHE SER ALA GLU PHE ASP GLU TRP LEU ALA PHE ASN SEQRES 24 A 341 ILE GLU MET ALA TRP SER HIS ARG ASN SER ASP HIS ILE SEQRES 25 A 341 VAL ASP GLY ASN TRP ALA GLY GLN LEU LEU SER GLY THR SEQRES 26 A 341 TYR GLU SER TRP SER SER ALA ALA ALA VAL GLN ALA LEU SEQRES 27 A 341 ASN GLY ILE FORMUL 2 HOH *214(H2 O) HELIX 1 1 SER A 39 PHE A 52 1 14 HELIX 2 2 ASP A 71 THR A 89 1 19 HELIX 3 3 ASP A 91 GLY A 114 1 24 HELIX 4 4 PHE A 122 GLY A 141 1 20 HELIX 5 5 ASN A 142 TRP A 161 1 20 HELIX 6 6 ALA A 182 LYS A 200 1 19 HELIX 7 7 ASP A 201 THR A 220 1 20 HELIX 8 8 THR A 241 GLY A 260 1 20 HELIX 9 9 ASN A 261 LEU A 279 1 19 HELIX 10 10 GLY A 297 GLY A 317 1 21 HELIX 11 11 TYR A 319 TRP A 338 1 20 HELIX 12 12 GLU A 361 LEU A 372 1 12 SHEET 1 AA 2 TRP A 53 ASP A 54 0 SHEET 2 AA 2 MET A 59 PHE A 60 -1 O MET A 59 N ASP A 54 SHEET 1 AB 3 THR A 179 ASN A 181 0 SHEET 2 AB 3 ARG A 229 GLU A 231 -1 O ILE A 230 N LYS A 180 SHEET 3 AB 3 GLY A 235 ALA A 236 -1 O GLY A 235 N GLU A 231 CISPEP 1 GLY A 290 PRO A 291 0 4.90 CRYST1 50.948 65.093 90.242 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 0.019628 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015363 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011081 0.00000