HEADER HYDROLASE 28-AUG-13 4MGS TITLE BIXYN10A CBM1 APO COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE GLYCOSYL HYDROLASE FAMILY 10; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 153-302; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES INTESTINALIS; SOURCE 3 ORGANISM_TAXID: 471870; SOURCE 4 STRAIN: DSM 17393; SOURCE 5 GENE: BACINT_04215; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENDO-XYLANASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.R.CHEKAN,S.K.NAIR REVDAT 4 28-FEB-24 4MGS 1 REMARK REVDAT 3 24-SEP-14 4MGS 1 JRNL REVDAT 2 03-SEP-14 4MGS 1 JRNL REVDAT 1 20-AUG-14 4MGS 0 JRNL AUTH M.ZHANG,J.R.CHEKAN,D.DODD,P.Y.HONG,L.RADLINSKI,V.REVINDRAN, JRNL AUTH 2 S.K.NAIR,R.I.MACKIE,I.CANN JRNL TITL XYLAN UTILIZATION IN HUMAN GUT COMMENSAL BACTERIA IS JRNL TITL 2 ORCHESTRATED BY UNIQUE MODULAR ORGANIZATION OF JRNL TITL 3 POLYSACCHARIDE-DEGRADING ENZYMES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 E3708 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 25136124 JRNL DOI 10.1073/PNAS.1406156111 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 14363 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1437 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 22.7945 - 3.8741 1.00 1396 156 0.1517 0.1467 REMARK 3 2 3.8741 - 3.0774 1.00 1325 147 0.1380 0.1623 REMARK 3 3 3.0774 - 2.6891 1.00 1304 145 0.1646 0.1829 REMARK 3 4 2.6891 - 2.4435 1.00 1286 142 0.1697 0.1992 REMARK 3 5 2.4435 - 2.2685 1.00 1280 143 0.1678 0.2041 REMARK 3 6 2.2685 - 2.1349 1.00 1286 143 0.1533 0.1961 REMARK 3 7 2.1349 - 2.0281 1.00 1259 140 0.1562 0.2247 REMARK 3 8 2.0281 - 1.9398 1.00 1275 141 0.1683 0.2015 REMARK 3 9 1.9398 - 1.8652 1.00 1280 142 0.1816 0.2290 REMARK 3 10 1.8652 - 1.8000 1.00 1235 138 0.2098 0.2952 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.000 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 : 0.006 1153 REMARK 3 ANGLE : 1.024 1557 REMARK 3 CHIRALITY : 0.073 164 REMARK 3 PLANARITY : 0.004 199 REMARK 3 DIHEDRAL : 15.636 414 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 4MGS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000081891. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14363 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 22.793 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 21.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.50100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.380 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5 M AMMONIUM SULFATE, 0.1 M BICINE, REMARK 280 PH 9.0, 42 MG/ML, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 26.36850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.32950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.36850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.32950 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 948 LIES ON A SPECIAL POSITION. 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 VAL A 153 REMARK 465 ASP A 154 REMARK 465 PRO A 155 REMARK 465 ASP A 156 REMARK 465 ALA A 157 REMARK 465 LYS A 158 REMARK 465 VAL A 159 REMARK 465 GLU A 301 REMARK 465 ALA A 302 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 967 O HOH A 981 1.86 REMARK 500 O HOH A 946 O HOH A 956 2.01 REMARK 500 O HOH A 890 O HOH A 916 2.08 REMARK 500 O HOH A 937 O HOH A 958 2.13 REMARK 500 O HOH A 891 O HOH A 894 2.14 REMARK 500 O HOH A 924 O HOH A 950 2.16 REMARK 500 O HOH A 952 O HOH A 966 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 982 O HOH A 984 1556 1.92 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 174 21.03 -141.62 REMARK 500 ASN A 260 -159.93 -140.85 REMARK 500 SER A 283 29.12 -150.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MGQ RELATED DB: PDB DBREF 4MGS A 153 302 UNP B3CET4 B3CET4_9BACE 153 302 SEQRES 1 A 150 VAL ASP PRO ASP ALA LYS VAL ASP LYS VAL ASP TYR GLU SEQRES 2 A 150 ILE ASP TYR SER THR ALA GLY TYR SER PHE TRP ASN GLU SEQRES 3 A 150 VAL ASN GLU GLU VAL LYS GLU THR THR THR ILE GLY LYS SEQRES 4 A 150 ASN ASP THR GLU GLY CYS LEU GLU ILE LYS THR SER VAL SEQRES 5 A 150 ALA ALA SER GLN ASN HIS PHE ILE GLN TYR HIS THR ALA SEQRES 6 A 150 ASP ASN LEU PRO ILE GLU ILE GLY LYS GLU TYR LYS LEU SEQRES 7 A 150 LYS MET MET VAL ARG GLY SER ALA GLU GLY LYS LEU ASN SEQRES 8 A 150 PHE GLY VAL GLY PRO TRP SER GLY ARG ALA GLU GLY SER SEQRES 9 A 150 PHE SER PHE ASN THR GLU TRP LYS GLU TYR GLU PHE SER SEQRES 10 A 150 PHE LYS ALA VAL ALA ASP GLY GLY HIS VAL MET THR GLN SEQRES 11 A 150 SER GLY LEU PHE VAL GLY THR ILE GLN ILE LYS TYR VAL SEQRES 12 A 150 LYS ILE THR HIS SER GLU ALA FORMUL 2 HOH *190(H2 O) HELIX 1 1 GLU A 181 GLU A 185 5 5 HELIX 2 2 GLN A 208 HIS A 210 5 3 SHEET 1 A 4 LYS A 161 ASP A 167 0 SHEET 2 A 4 GLY A 288 HIS A 299 -1 O HIS A 299 N LYS A 161 SHEET 3 A 4 CYS A 197 THR A 202 -1 N ILE A 200 O ILE A 290 SHEET 4 A 4 THR A 187 ASN A 192 -1 N ASN A 192 O CYS A 197 SHEET 1 B 4 LYS A 161 ASP A 167 0 SHEET 2 B 4 GLY A 288 HIS A 299 -1 O HIS A 299 N LYS A 161 SHEET 3 B 4 GLU A 227 GLY A 236 -1 N LYS A 231 O LYS A 296 SHEET 4 B 4 LYS A 264 LYS A 271 -1 O TYR A 266 N MET A 232 SHEET 1 C 5 ASN A 177 VAL A 179 0 SHEET 2 C 5 ILE A 212 HIS A 215 -1 O GLN A 213 N GLU A 178 SHEET 3 C 5 HIS A 278 GLN A 282 -1 O THR A 281 N TYR A 214 SHEET 4 C 5 GLY A 240 GLY A 247 -1 N ASN A 243 O GLN A 282 SHEET 5 C 5 ALA A 253 PHE A 259 -1 O ALA A 253 N VAL A 246 CRYST1 52.737 90.659 30.998 90.00 90.00 90.00 P 21 21 2 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 0.018962 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011030 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032260 0.00000