PDB Short entry for 2JIC HEADER HYDROLASE 27-FEB-07 2JIC TITLE HIGH RESOLUTION STRUCTURE OF XYLANASE-II FROM ONE MICRON BEAM TITLE 2 EXPERIMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLANASE-II; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.8 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHODERMA LONGIBRACHIATUM; SOURCE 3 ORGANISM_TAXID: 5548 KEYWDS HYDROLASE, ENDONUCLEASE, XYLAN DEGRADATION, FUNGI, XYLAN, MICROBEAM, KEYWDS 2 GLYCOSIDASE EXPDTA X-RAY DIFFRACTION AUTHOR R.MOUKHAMETZIANOV,M.BURGHAMMER,P.C.EDWARDS,S.PETITDEMANGE,D.POPOV, AUTHOR 2 M.FRANSEN,G.F.SCHERTLER,C.RIEKEL REVDAT 4 13-DEC-23 2JIC 1 REMARK REVDAT 3 06-JUN-12 2JIC 1 JRNL REMARK VERSN FORMUL REVDAT 2 24-FEB-09 2JIC 1 VERSN REVDAT 1 13-MAY-08 2JIC 0 JRNL AUTH R.MOUKHAMETZIANOV,M.BURGHAMMER,P.C.EDWARDS,S.PETITDEMANGE, JRNL AUTH 2 D.POPOV,M.FRANSEN,G.MCMULLAN,G.F.SCHERTLER,C.RIEKEL JRNL TITL PROTEIN CRYSTALLOGRAPHY WITH A MICROMETRE-SIZED JRNL TITL 2 SYNCHROTRON-RADIATION BEAM. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 64 158 2008 JRNL REFN ISSN 0907-4449 JRNL PMID 18219115 JRNL DOI 10.1107/S090744490705812X REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1105231.340 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 26747 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1297 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4172 REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE : 0.2120 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 205 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1472 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.34000 REMARK 3 B22 (A**2) : 0.27000 REMARK 3 B33 (A**2) : -1.62000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.76000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.07 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.09 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.48 REMARK 3 BSOL : 54.48 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: XYLANASE-II WAS USED AS A TEST CRYSTAL REMARK 3 FOR THE ONE MICRON SIZE BEAM CRYSTALLOGRAPHY REMARK 4 REMARK 4 2JIC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1290031472. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : SI-111 DOUBLE CRYSTAL REMARK 200 OPTICS : KB MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26872 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.16000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2D97 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULPHATE, 100 MM MES PH REMARK 280 5.5 AND 0.5 M MGCL2 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 19.41500 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 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 MET A 1 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 THR A 95 -52.35 70.27 REMARK 500 ASP A 170 -139.76 -109.84 REMARK 500 REMARK 500 REMARK: NULL DBREF 2JIC A 1 190 PDB 2JIC 2JIC 1 190 SEQRES 1 A 190 MET 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 FORMUL 2 HOH *138(H2 O) HELIX 1 1 THR A 152 GLN A 162 1 11 SHEET 1 AA 9 GLY A 6 ASN A 10 0 SHEET 2 AA 9 TYR A 13 ASN A 19 -1 O TYR A 13 N ASN A 10 SHEET 3 AA 9 ASN A 44 TRP A 51 -1 O VAL A 46 N TRP A 18 SHEET 4 AA 9 THR A 168 TYR A 179 -1 O GLN A 172 N TRP A 51 SHEET 5 AA 9 SER A 72 ARG A 81 -1 O TYR A 73 N GLU A 177 SHEET 6 AA 9 ILE A 85 PHE A 93 -1 O ILE A 85 N SER A 80 SHEET 7 AA 9 ALA A 132 ARG A 141 1 O TYR A 135 N GLU A 86 SHEET 8 AA 9 SER A 113 GLN A 125 -1 O ASP A 116 N VAL A 140 SHEET 9 AA 9 THR A 103 SER A 110 -1 O THR A 103 N ARG A 119 SHEET 1 AB 5 VAL A 25 ASN A 29 0 SHEET 2 AB 5 GLN A 34 TRP A 39 -1 O SER A 36 N THR A 28 SHEET 3 AB 5 SER A 182 SER A 190 -1 O GLY A 183 N TRP A 39 SHEET 4 AB 5 VAL A 59 ASN A 69 -1 O ASN A 61 N SER A 190 SHEET 5 AB 5 GLY A 148 ASN A 151 -1 O GLY A 148 N PHE A 62 CISPEP 1 GLN A 52 PRO A 53 0 0.08 CISPEP 2 ASN A 82 PRO A 83 0 0.54 CRYST1 40.570 38.830 57.340 90.00 110.61 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 0.024649 0.000000 0.009270 0.00000 SCALE2 0.000000 0.025753 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018632 0.00000