HEADER HYDROLASE 20-JUN-23 8JST TITLE GH11 FAMILY XYLANASE RMXYLCD FROM THE COMPOST-SOIL METAGENOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-BETA-1,4-XYLANASE RMXYLCD; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.8; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: COMPOST METAGENOME; SOURCE 3 ORGANISM_TAXID: 702656; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS GLYCOSIDE HYDROLASE, THERMOSTABLE XYLANASE, DISULFIDE BOND, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.N.WU,N.Y.ZHANG,Q.WAN REVDAT 2 13-NOV-24 8JST 1 REMARK REVDAT 1 26-JUN-24 8JST 0 JRNL AUTH S.N.WU,Q.WAN JRNL TITL GH11 FAMILY XYLANASE RMXYLCD FROM THE COMPOST-SOIL JRNL TITL 2 METAGENOME JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.230 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 91108 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.710 REMARK 3 FREE R VALUE TEST SET COUNT : 2465 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 3.1200 - 2.7200 0.92 4827 126 0.0000 0.1514 REMARK 3 2 2.7200 - 2.4800 0.92 4860 140 0.0000 0.1441 REMARK 3 3 2.4800 - 2.3000 0.93 4898 130 0.1740 0.1952 REMARK 3 4 2.3000 - 2.1600 0.94 4928 134 0.1658 0.1919 REMARK 3 5 2.1600 - 2.0500 0.94 4956 138 0.1656 0.1697 REMARK 3 6 2.0500 - 1.9700 0.94 4943 130 0.0000 0.1675 REMARK 3 7 1.9700 - 1.8900 0.94 4986 138 0.1678 0.1861 REMARK 3 8 1.8900 - 1.8200 0.95 4975 142 0.1730 0.2018 REMARK 3 9 1.8200 - 1.7700 0.95 4995 138 0.1854 0.2147 REMARK 3 10 1.7700 - 1.7200 0.95 4965 136 0.0000 0.1509 REMARK 3 11 1.7200 - 1.6700 0.95 4997 142 0.2023 0.2450 REMARK 3 12 1.6700 - 1.6300 0.95 5026 137 0.2135 0.2204 REMARK 3 13 1.6300 - 1.5900 0.95 4977 142 0.0000 0.1863 REMARK 3 14 1.5900 - 1.5600 0.95 5009 133 0.2549 0.3190 REMARK 3 15 1.5600 - 1.5300 0.96 5047 145 0.2833 0.3067 REMARK 3 16 1.5300 - 1.5000 0.96 5087 144 0.0000 0.3369 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) : 0.166 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.475 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.01 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 : 0.009 1556 REMARK 3 ANGLE : 1.551 2122 REMARK 3 CHIRALITY : 0.086 208 REMARK 3 PLANARITY : 0.003 277 REMARK 3 DIHEDRAL : 16.371 530 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 8JST COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300038788. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 131697 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 18.90 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.8000 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 (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.06100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 1500, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 69.88200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.50500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.50500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 104.82300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.50500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.50500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.94100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.50500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.50500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 104.82300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.50500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.50500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.94100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 69.88200 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 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 521 LIES ON A SPECIAL POSITION. 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 OG SER A 1 NH1 ARG A 123 6545 1.53 REMARK 500 REMARK 500 REMARK: NULL 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 PRO A 84 C - N - CD ANGL. DEV. = 14.6 DEGREES REMARK 500 PRO A 100 C - N - CD ANGL. DEV. = 15.1 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 45 -69.85 -104.48 REMARK 500 PRO A 100 55.31 -103.39 REMARK 500 ASN A 172 -144.72 -108.03 REMARK 500 REMARK 500 REMARK: NULL DBREF 8JST A 1 192 PDB 8JST 8JST 1 192 SEQRES 1 A 192 SER GLY SER CYS LEU THR ASN ASN GLN THR GLY THR HIS SEQRES 2 A 192 ASP GLY TYR TYR TYR SER PHE TRP LYS ASP SER GLY ASN SEQRES 3 A 192 VAL THR PHE CYS LEU GLN SER GLY GLY ARG TYR THR SER SEQRES 4 A 192 GLN TRP SER ASN ILE ASN ASN TRP VAL GLY GLY LYS GLY SEQRES 5 A 192 TRP ASN PRO GLY GLY ARG ARG THR VAL THR TYR SER GLY SEQRES 6 A 192 THR PHE ASN PRO ASN GLY ASN ALA TYR LEU THR LEU TYR SEQRES 7 A 192 GLY TRP THR THR ASN PRO LEU VAL GLU TYR TYR ILE VAL SEQRES 8 A 192 ASP ASN TRP GLY THR TYR ARG PRO PRO GLY GLY GLN GLY SEQRES 9 A 192 TYR MET GLY THR VAL ASN SER ASP GLY GLY THR TYR ASP SEQRES 10 A 192 ILE TYR ARG THR GLN ARG VAL ASN ALA PRO CYS ILE THR SEQRES 11 A 192 GLY ASN ASN CYS THR PHE TRP GLN TYR TRP SER VAL ARG SEQRES 12 A 192 GLN GLN ARG ARG THR GLY GLY THR ILE THR THR GLY ASN SEQRES 13 A 192 HIS PHE ASP ALA TRP ALA SER LEU GLY MET ASN LEU GLY SEQRES 14 A 192 GLN HIS ASN TYR MET VAL MET ALA THR GLU GLY TYR GLN SEQRES 15 A 192 SER SER GLY SER SER ASP ILE THR VAL GLY HET GOL A 201 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *221(H2 O) HELIX 1 AA1 THR A 154 LEU A 164 1 11 SHEET 1 AA1 6 CYS A 4 LEU A 5 0 SHEET 2 AA1 6 ASN A 26 LEU A 31 -1 O PHE A 29 N LEU A 5 SHEET 3 AA1 6 ARG A 36 SER A 42 -1 O GLN A 40 N THR A 28 SHEET 4 AA1 6 SER A 184 VAL A 191 -1 O SER A 187 N SER A 39 SHEET 5 AA1 6 THR A 60 ASN A 70 -1 N ASN A 68 O SER A 186 SHEET 6 AA1 6 GLY A 150 THR A 153 -1 O ILE A 152 N VAL A 61 SHEET 1 AA2 9 GLN A 9 HIS A 13 0 SHEET 2 AA2 9 TYR A 16 LYS A 22 -1 O TYR A 16 N HIS A 13 SHEET 3 AA2 9 ASN A 46 TRP A 53 -1 O GLY A 52 N TYR A 17 SHEET 4 AA2 9 GLN A 170 TYR A 181 -1 O MET A 174 N TRP A 53 SHEET 5 AA2 9 ALA A 73 THR A 82 -1 N TYR A 78 O VAL A 175 SHEET 6 AA2 9 VAL A 86 TRP A 94 -1 O TYR A 88 N GLY A 79 SHEET 7 AA2 9 GLY A 131 ARG A 143 1 O ARG A 143 N VAL A 91 SHEET 8 AA2 9 GLY A 114 CYS A 128 -1 N ALA A 126 O CYS A 134 SHEET 9 AA2 9 TYR A 105 SER A 111 -1 N GLY A 107 O ILE A 118 SSBOND 1 CYS A 4 CYS A 30 1555 1555 2.17 SSBOND 2 CYS A 128 CYS A 134 1555 1555 2.18 CISPEP 1 ASN A 54 PRO A 55 0 2.56 CISPEP 2 ASN A 83 PRO A 84 0 0.93 CISPEP 3 PRO A 99 PRO A 100 0 -4.22 CRYST1 67.010 67.010 139.764 90.00 90.00 90.00 P 43 21 2 8 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 0.014923 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014923 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007155 0.00000