HEADER METAL BINDING PROTEIN 09-NOV-20 7AX7 TITLE CRYSTAL STRUCTURE OF THE XYL-CE4 DOMAIN OF A MULTIDOMAIN XYLANASE FROM TITLE 2 THE HINDGUT METAGENOME OF TRINERVITERMES TRINERVOIDES 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: UNCULTURED BACTERIUM; SOURCE 3 ORGANISM_TAXID: 77133; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS XYL-CE4 USES CO2+ TO CLEAVE ACETYL GROUPS FROM ACETYLATED XYLAN KEYWDS 2 MOLECULES. AS PART OF A MULTIDOMAIN ASSEMBLY, CE4 FUNCTIONS KEYWDS 3 INDEPENDENTLY OF OTHER DOMAIN COMPONENTS., METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.ANYE,W.D.SCHUBERT REVDAT 3 31-JAN-24 7AX7 1 REMARK REVDAT 2 29-JUN-22 7AX7 1 JRNL REVDAT 1 18-NOV-20 7AX7 0 JRNL AUTH V.ANYE,R.F.KRUGER,W.D.SCHUBERT JRNL TITL STRUCTURAL AND BIOPHYSICAL CHARACTERIZATION OF THE JRNL TITL 2 MULTIDOMAIN XYLANASE XYL. JRNL REF PLOS ONE V. 17 69188 2022 JRNL REFN ESSN 1932-6203 JRNL PMID 35657930 JRNL DOI 10.1371/JOURNAL.PONE.0269188 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHASER REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.438 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13512 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.055 REMARK 3 FREE R VALUE TEST SET COUNT : 683 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.06 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2534 REMARK 3 BIN R VALUE (WORKING SET) : 0.2592 REMARK 3 BIN FREE R VALUE : 0.3718 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 127 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1610 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 247 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.14 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7AX7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1292112101. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK 1.12_2829 REMARK 200 DATA SCALING SOFTWARE : D*TREK 1.12_2829, D*TREK REMARK 200 1.12_2829 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13512 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 23.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: 2C71 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML IN 20 MM TRIS-HCL PH 7.5, 10 REMARK 280 MM NACL, 8 % (W/V) PEG 4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292.2K 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 20.06500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.05000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.85000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.05000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.06500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.85000 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: 380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 582 REMARK 465 HIS A 788 REMARK 465 HIS A 789 REMARK 465 HIS A 790 REMARK 465 HIS A 791 REMARK 465 HIS A 792 REMARK 465 HIS A 793 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 ASP A 593 -0.46 99.15 REMARK 500 SER A 644 176.87 79.98 REMARK 500 GLN A 701 -83.12 -109.37 REMARK 500 ASP A 707 30.19 -97.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1146 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH A1147 DISTANCE = 8.46 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 801 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 593 OD1 REMARK 620 2 HIS A 643 NE2 89.4 REMARK 620 3 HIS A 647 NE2 96.2 91.9 REMARK 620 4 ACT A 802 O 106.9 87.8 156.9 REMARK 620 5 ACT A 802 OXT 165.2 94.6 97.9 59.1 REMARK 620 N 1 2 3 4 DBREF1 7AX7 A 582 787 UNP A0A140HJ20_9BACT DBREF2 7AX7 A A0A140HJ20 582 787 SEQADV 7AX7 SER A 708 UNP A0A140HJ2 TRP 708 VARIANT SEQADV 7AX7 HIS A 788 UNP A0A140HJ2 EXPRESSION TAG SEQADV 7AX7 HIS A 789 UNP A0A140HJ2 EXPRESSION TAG SEQADV 7AX7 HIS A 790 UNP A0A140HJ2 EXPRESSION TAG SEQADV 7AX7 HIS A 791 UNP A0A140HJ2 EXPRESSION TAG SEQADV 7AX7 HIS A 792 UNP A0A140HJ2 EXPRESSION TAG SEQADV 7AX7 HIS A 793 UNP A0A140HJ2 EXPRESSION TAG SEQRES 1 A 212 GLY ASN GLU LYS LEU ILE ALA LEU THR PHE ASP ASP GLY SEQRES 2 A 212 PRO SER SER THR THR SER ASP VAL LEU ASP ILE LEU GLU SEQRES 3 A 212 ARG TYR GLY VAL LYS ALA THR PHE PHE LEU ILE GLY GLN SEQRES 4 A 212 ASN VAL ASN SER ASN THR LEU SER ILE MET GLN ARG GLN SEQRES 5 A 212 VAL ARG MET GLY CYS GLU LEU ALA SER HIS SER TYR THR SEQRES 6 A 212 HIS GLN ASP MET THR ASN MET SER ALA GLN ASN ILE ARG SEQRES 7 A 212 ASN GLU MET GLU TRP THR SER SER ALA ILE LYS ASN SER SEQRES 8 A 212 VAL GLY VAL ASP VAL LYS PHE PHE ARG PRO PRO TYR ILE SEQRES 9 A 212 ALA VAL ASN ASN THR MET TYR GLN ASN ILE ASP TYR PRO SEQRES 10 A 212 PHE ILE GLN GLY THR LEU ILE ASN ASP SER GLU ASN SER SEQRES 11 A 212 THR SER VAL GLN GLN ARG VAL ASN ASN ALA LEU GLY ALA SEQRES 12 A 212 ALA LYS ASP GLY GLN ILE ILE LEU LEU HIS ASP PHE GLN SEQRES 13 A 212 GLY ASN SER GLN THR VAL GLN ALA LEU PRO GLN ILE ILE SEQRES 14 A 212 GLU GLY LEU LYS ASN GLN GLY TYR THR PHE VAL THR VAL SEQRES 15 A 212 SER GLU LEU PHE GLU LYS LYS GLY VAL ASN PRO ASN VAL SEQRES 16 A 212 GLU TYR LYS ILE TRP SER ASN ALA ASN GLY GLN HIS HIS SEQRES 17 A 212 HIS HIS HIS HIS HET CO A 801 1 HET ACT A 802 4 HETNAM CO COBALT (II) ION HETNAM ACT ACETATE ION FORMUL 2 CO CO 2+ FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *247(H2 O) HELIX 1 AA1 SER A 596 GLY A 610 1 15 HELIX 2 AA2 ILE A 618 VAL A 622 5 5 HELIX 3 AA3 THR A 626 MET A 636 1 11 HELIX 4 AA4 ASP A 649 MET A 653 5 5 HELIX 5 AA5 SER A 654 GLY A 674 1 21 HELIX 6 AA6 PRO A 682 ALA A 686 5 5 HELIX 7 AA7 ASN A 688 ILE A 695 1 8 HELIX 8 AA8 SER A 713 ALA A 725 1 13 HELIX 9 AA9 ASN A 739 GLN A 756 1 18 HELIX 10 AB1 THR A 762 GLY A 771 1 10 SHEET 1 AA1 5 GLU A 639 SER A 642 0 SHEET 2 AA1 5 THR A 614 LEU A 617 1 N PHE A 615 O GLU A 639 SHEET 3 AA1 5 LYS A 585 ASP A 592 1 N PHE A 591 O THR A 614 SHEET 4 AA1 5 GLN A 729 HIS A 734 1 O ILE A 731 N ALA A 588 SHEET 5 AA1 5 THR A 703 LEU A 704 1 N THR A 703 O ILE A 730 SHEET 1 AA2 4 GLU A 639 SER A 642 0 SHEET 2 AA2 4 THR A 614 LEU A 617 1 N PHE A 615 O GLU A 639 SHEET 3 AA2 4 LYS A 585 ASP A 592 1 N PHE A 591 O THR A 614 SHEET 4 AA2 4 TYR A 758 PHE A 760 1 O THR A 759 N LYS A 585 SHEET 1 AA3 2 PHE A 699 ILE A 700 0 SHEET 2 AA3 2 ILE A 780 TRP A 781 1 O TRP A 781 N PHE A 699 LINK OD1 ASP A 593 CO CO A 801 1555 1555 2.14 LINK NE2 HIS A 643 CO CO A 801 1555 1555 2.24 LINK NE2 HIS A 647 CO CO A 801 1555 1555 2.16 LINK CO CO A 801 O ACT A 802 1555 1555 2.26 LINK CO CO A 801 OXT ACT A 802 1555 1555 2.35 CISPEP 1 GLY A 594 PRO A 595 0 -2.14 CRYST1 40.130 59.700 86.100 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 0.024919 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016750 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011614 0.00000