HEADER HYDROLASE 06-MAY-16 5JRN TITLE CRYSTAL STRUCTURE OF A XYLANASE IN COMPLEX WITH A MONOSACCHARIDE AT TITLE 2 2.84 ANGSTROEM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.8; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FUSARIUM OXYSPORUM F. SP. VASINFECTUM 25433; SOURCE 3 ORGANISM_TAXID: 1089449; SOURCE 4 GENE: FOTG_15646; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PETM-11 KEYWDS XYLANASE, COMPLEX, GH11, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.GOMEZ,A.M.PAYNE,M.SAVKO,G.C.FOX,W.E.SHEPARD,F.J.FERNANDEZ,M.C.VEGA REVDAT 4 10-JAN-24 5JRN 1 HETSYN REVDAT 3 29-JUL-20 5JRN 1 REMARK SITE ATOM REVDAT 2 13-SEP-17 5JRN 1 REMARK REVDAT 1 24-MAY-17 5JRN 0 JRNL AUTH S.GOMEZ,A.M.PAYNE,M.SAVKO,G.C.FOX,W.E.SHEPARD,F.J.FERNANDEZ, JRNL AUTH 2 M.C.VEGA JRNL TITL CRYSTAL STRUCTURE OF A XYLANASE IN COMPLEX WITH A JRNL TITL 2 MONOSACCHARIDE AT 2.84 ANGSTROEM RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 2.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 4760 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 239 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 48.8072 - 3.5786 1.00 2317 123 0.1800 0.2116 REMARK 3 2 3.5786 - 2.8406 1.00 2204 116 0.2585 0.2493 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.35 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 : 0.002 1563 REMARK 3 ANGLE : 0.891 2116 REMARK 3 CHIRALITY : 0.027 209 REMARK 3 PLANARITY : 0.007 272 REMARK 3 DIHEDRAL : 14.278 540 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 5JRN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221121. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98009 REMARK 200 MONOCHROMATOR : CHANNEL-CUT SI(111) REMARK 200 OPTICS : CHANNEL-CUT SI(111) + KB REMARK 200 FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS NOVEMBER 3, 2014 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4766 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.840 REMARK 200 RESOLUTION RANGE LOW (A) : 48.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.25200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 0.88400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.730 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.6.0 REMARK 200 STARTING MODEL: 5JRM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE PH 5, VARYING REMARK 280 AMMONIUM SULFATE CONCENTRATIONS, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 52.85000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.05000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 52.85000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.05000 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 TOTAL BURIED SURFACE AREA: 1190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 KCAL/MOL 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 GLY A -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 ASP A 0 REMARK 465 LYS A 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 THR A 94 CA - C - N ANGL. DEV. = -15.8 DEGREES 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 ASN A 81 73.66 52.09 REMARK 500 THR A 94 -78.15 -25.62 REMARK 500 ASP A 169 -136.02 -99.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 THR A 94 13.50 REMARK 500 REMARK 500 REMARK: NULL DBREF 5JRN A 0 190 UNP X0M5X0 X0M5X0_FUSOX 42 232 SEQADV 5JRN GLY A -3 UNP X0M5X0 EXPRESSION TAG SEQADV 5JRN ALA A -2 UNP X0M5X0 EXPRESSION TAG SEQADV 5JRN MET A -1 UNP X0M5X0 EXPRESSION TAG SEQRES 1 A 194 GLY ALA MET ASP LYS ARG THR GLN PRO THR THR GLY THR SEQRES 2 A 194 SER GLY GLY TYR TYR PHE SER PHE TRP THR ASP THR PRO SEQRES 3 A 194 ASN SER VAL THR TYR THR ASN GLY ASN GLY GLY GLN PHE SEQRES 4 A 194 SER MET GLN TRP SER GLY ASN GLY ASN HIS VAL GLY GLY SEQRES 5 A 194 LYS GLY TRP MET PRO GLY THR SER ARG THR ILE LYS TYR SEQRES 6 A 194 SER GLY SER TYR ASN PRO ASN GLY ASN SER TYR LEU ALA SEQRES 7 A 194 VAL TYR GLY TRP THR ARG ASN PRO LEU ILE GLU TYR TYR SEQRES 8 A 194 ILE VAL GLU ASN PHE GLY THR TYR ASN PRO SER SER GLY SEQRES 9 A 194 GLY GLN LYS LYS GLY GLU VAL ASN VAL ASP GLY SER VAL SEQRES 10 A 194 TYR ASP ILE TYR VAL SER THR ARG VAL ASN ALA PRO SER SEQRES 11 A 194 ILE ASP GLY ASN LYS THR PHE GLN GLN TYR TRP SER VAL SEQRES 12 A 194 ARG ARG ASN LYS ARG SER SER GLY SER VAL ASN THR GLY SEQRES 13 A 194 ALA HIS PHE GLN ALA TRP LYS ASN VAL GLY LEU ASN LEU SEQRES 14 A 194 GLY THR HIS ASP TYR GLN ILE LEU ALA VAL GLU GLY TYR SEQRES 15 A 194 TYR SER SER GLY SER ALA SER MET THR VAL SER GLN HET GOL A 201 6 HET GOL A 202 6 HET GOL A 203 6 HET GOL A 204 6 HET GOL A 205 6 HET GOL A 206 6 HET GOL A 207 6 HET 6MJ A 208 11 HETNAM GOL GLYCEROL HETNAM 6MJ METHYL BETA-D-XYLOPYRANOSIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN 6MJ METHYL BETA-D-XYLOSIDE; METHYL D-XYLOSIDE; METHYL HETSYN 2 6MJ XYLOSIDE FORMUL 2 GOL 7(C3 H8 O3) FORMUL 9 6MJ C6 H12 O5 FORMUL 10 HOH *21(H2 O) HELIX 1 AA1 THR A 151 VAL A 161 1 11 SHEET 1 AA1 9 THR A 6 SER A 10 0 SHEET 2 AA1 9 TYR A 13 THR A 19 -1 O TYR A 13 N SER A 10 SHEET 3 AA1 9 ASN A 44 TRP A 51 -1 O VAL A 46 N TRP A 18 SHEET 4 AA1 9 THR A 167 TYR A 178 -1 O LEU A 173 N LYS A 49 SHEET 5 AA1 9 SER A 71 ARG A 80 -1 N TRP A 78 O ASP A 169 SHEET 6 AA1 9 ILE A 84 PHE A 92 -1 O ASN A 91 N LEU A 73 SHEET 7 AA1 9 GLY A 129 ARG A 140 1 O ARG A 140 N VAL A 89 SHEET 8 AA1 9 SER A 112 SER A 126 -1 N ALA A 124 O LYS A 131 SHEET 9 AA1 9 GLN A 102 VAL A 109 -1 N LYS A 104 O ILE A 116 SHEET 1 AA2 5 VAL A 25 ASN A 29 0 SHEET 2 AA2 5 GLN A 34 TRP A 39 -1 O SER A 36 N THR A 28 SHEET 3 AA2 5 SER A 181 SER A 189 -1 O GLY A 182 N TRP A 39 SHEET 4 AA2 5 THR A 58 ASN A 68 -1 N ASN A 68 O SER A 181 SHEET 5 AA2 5 GLY A 147 ASN A 150 -1 O GLY A 147 N TYR A 61 CISPEP 1 MET A 52 PRO A 53 0 -1.17 CISPEP 2 ASN A 81 PRO A 82 0 2.70 CRYST1 105.700 36.100 48.800 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 0.009461 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027701 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020492 0.00000