HEADER HYDROLASE 26-MAY-16 5K7P TITLE MICROED STRUCTURE OF XYLANASE AT 2.3 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: XYLANASE 2,1,4-BETA-D-XYLAN XYLANOHYDROLASE 2; COMPND 5 EC: 3.2.1.8 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HYPOCREA JECORINA; SOURCE 3 ORGANISM_COMMON: TRICHODERMA REESEI; SOURCE 4 ORGANISM_TAXID: 51453 KEYWDS HYDROLASE EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR M.J.DE LA CRUZ,J.HATTNE,D.SHI,P.SEIDLER,J.RODRIGUEZ,F.E.REYES, AUTHOR 2 M.R.SAWAYA,D.CASCIO,D.EISENBERG,T.GONEN REVDAT 5 28-FEB-24 5K7P 1 REMARK REVDAT 4 22-AUG-18 5K7P 1 REMARK REVDAT 3 18-JUL-18 5K7P 1 REMARK REVDAT 2 12-APR-17 5K7P 1 JRNL REVDAT 1 05-APR-17 5K7P 0 JRNL AUTH M.J.DE LA CRUZ,J.HATTNE,D.SHI,P.SEIDLER,J.RODRIGUEZ, JRNL AUTH 2 F.E.REYES,M.R.SAWAYA,D.CASCIO,S.C.WEISS,S.K.KIM,C.S.HINCK, JRNL AUTH 3 A.P.HINCK,G.CALERO,D.EISENBERG,T.GONEN JRNL TITL ATOMIC-RESOLUTION STRUCTURES FROM FRAGMENTED PROTEIN JRNL TITL 2 CRYSTALS WITH THE CRYOEM METHOD MICROED. JRNL REF NAT. METHODS V. 14 399 2017 JRNL REFN ESSN 1548-7105 JRNL PMID 28192420 JRNL DOI 10.1038/NMETH.4178 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.4 REMARK 3 NUMBER OF REFLECTIONS : 7734 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 369 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 25.5508 - 3.3156 0.85 2622 135 0.1675 0.2014 REMARK 3 2 3.3156 - 2.6326 0.87 2546 146 0.2731 0.3236 REMARK 3 3 2.6326 - 2.3000 0.75 2197 88 0.3540 0.3895 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) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.950 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 : 0.002 1527 REMARK 3 ANGLE : 0.496 2084 REMARK 3 CHIRALITY : 0.043 207 REMARK 3 PLANARITY : 0.003 275 REMARK 3 DIHEDRAL : 10.687 841 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 5K7P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000221817. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : NULL REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 10664 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 240 RESOLUTION RANGE LOW (A) : 25.550 REMARK 240 DATA SCALING SOFTWARE : NULL REMARK 240 COMPLETENESS FOR RANGE (%) : 66.6 REMARK 240 DATA REDUNDANCY : 3.600 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.90 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.94 REMARK 240 COMPLETENESS FOR SHELL (%) : 20.4 REMARK 240 DATA REDUNDANCY IN SHELL : 1.60 REMARK 240 R MERGE FOR SHELL (I) : 2.47700 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : 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 24.08050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.90600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.87600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.90600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.08050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.87600 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: 240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 115 76.02 53.65 REMARK 500 ASP A 203 -137.11 -98.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-8218 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8216 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8217 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8219 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8220 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8221 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8222 RELATED DB: EMDB REMARK 900 RELATED ID: 5K7N RELATED DB: PDB REMARK 900 RELATED ID: 5K7O RELATED DB: PDB REMARK 900 RELATED ID: 5K7Q RELATED DB: PDB REMARK 900 RELATED ID: 5K7R RELATED DB: PDB REMARK 900 RELATED ID: 5K7S RELATED DB: PDB REMARK 900 RELATED ID: 5K7T RELATED DB: PDB DBREF 5K7P A 34 223 UNP P36217 XYN2_HYPJR 34 223 SEQRES 1 A 190 GLN THR ILE GLN PRO GLY THR GLY TYR ASN ASN GLY TYR SEQRES 2 A 190 PHE TYR SER TYR TRP ASN ASP GLY HIS GLY GLY VAL THR SEQRES 3 A 190 TYR THR ASN GLY PRO GLY GLY GLN PHE SER VAL ASN TRP SEQRES 4 A 190 SER ASN SER GLY ASN PHE VAL GLY GLY LYS GLY TRP GLN SEQRES 5 A 190 PRO GLY THR LYS ASN LYS VAL ILE ASN PHE SER GLY SER SEQRES 6 A 190 TYR ASN PRO ASN GLY ASN SER TYR LEU SER VAL TYR GLY SEQRES 7 A 190 TRP SER ARG ASN PRO LEU ILE GLU TYR TYR ILE VAL GLU SEQRES 8 A 190 ASN PHE GLY THR TYR ASN PRO SER THR GLY ALA THR LYS SEQRES 9 A 190 LEU GLY GLU VAL THR SER ASP GLY SER VAL TYR ASP ILE SEQRES 10 A 190 TYR ARG THR GLN ARG VAL ASN GLN PRO SER ILE ILE GLY SEQRES 11 A 190 THR ALA THR PHE TYR GLN TYR TRP SER VAL ARG ARG ASN SEQRES 12 A 190 HIS ARG SER SER GLY SER VAL ASN THR ALA ASN HIS PHE SEQRES 13 A 190 ASN ALA TRP ALA GLN GLN GLY LEU THR LEU GLY THR MET SEQRES 14 A 190 ASP TYR GLN ILE VAL ALA VAL GLU GLY TYR PHE SER SER SEQRES 15 A 190 GLY SER ALA SER ILE THR VAL SER HET IOD A 301 1 HET IOD A 302 1 HETNAM IOD IODIDE ION FORMUL 2 IOD 2(I 1-) FORMUL 4 HOH *23(H2 O) HELIX 1 AA1 THR A 185 GLN A 195 1 11 SHEET 1 AA1 9 GLY A 39 ASN A 43 0 SHEET 2 AA1 9 TYR A 46 ASN A 52 -1 O TYR A 50 N GLY A 39 SHEET 3 AA1 9 ASN A 77 TRP A 84 -1 O GLY A 83 N PHE A 47 SHEET 4 AA1 9 THR A 201 TYR A 212 -1 O VAL A 207 N LYS A 82 SHEET 5 AA1 9 SER A 105 ARG A 114 -1 N ARG A 114 O THR A 201 SHEET 6 AA1 9 ILE A 118 PHE A 126 -1 O GLU A 124 N LEU A 107 SHEET 7 AA1 9 ALA A 165 ARG A 174 1 O TYR A 170 N TYR A 121 SHEET 8 AA1 9 SER A 146 GLN A 158 -1 N THR A 153 O GLN A 169 SHEET 9 AA1 9 THR A 136 SER A 143 -1 N LEU A 138 O ILE A 150 SHEET 1 AA2 5 VAL A 58 ASN A 62 0 SHEET 2 AA2 5 GLN A 67 TRP A 72 -1 O SER A 69 N THR A 61 SHEET 3 AA2 5 SER A 215 SER A 223 -1 O GLY A 216 N TRP A 72 SHEET 4 AA2 5 VAL A 92 ASN A 102 -1 N ASN A 102 O SER A 215 SHEET 5 AA2 5 GLY A 181 ASN A 184 -1 O GLY A 181 N PHE A 95 CISPEP 1 GLN A 85 PRO A 86 0 -1.95 CISPEP 2 ASN A 115 PRO A 116 0 1.63 SITE 1 AC1 1 SER A 179 SITE 1 AC2 2 VAL A 156 GLN A 158 CRYST1 48.161 59.752 69.812 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 0.020764 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016736 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014324 0.00000