HEADER HYDROLASE 31-JUL-15 5CZL TITLE CRYSTAL STRUCTURE OF A NOVEL GH8 ENDO-BETA-1,4-GLUCANASE FROM AN TITLE 2 ACHATINA FULICA GUT METAGENOMIC LIBRARY COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCANASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RAOULTELLA ORNITHINOLYTICA; SOURCE 3 ORGANISM_TAXID: 54291; SOURCE 4 GENE: TE10_01090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCOSYL HYDROLASE FAMILY 8, ENDO-BETA-1, 4-GLUCANASE, ACHATINA KEYWDS 2 FULICA GUT METAGENOME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.M.N.SCAPIN,F.H.M.SOUZA,L.M.ZANPHORLIN,T.S.ALMEIDA,Y.B.SADE, AUTHOR 2 A.M.CARDOSO,G.L.PINHEIRO,M.T.MURAKAMI REVDAT 2 06-MAR-24 5CZL 1 REMARK REVDAT 1 03-AUG-16 5CZL 0 JRNL AUTH S.M.N.SCAPIN,F.H.M.SOUZA,L.M.ZANPHORLIN,T.ALMEIDA, JRNL AUTH 2 G.L.PINHEIRO,M.T.MURAKAMI JRNL TITL CRYSTAL STRUCTURE OF A NOVEL GH8 ENDO-BETA-1,4-GLUCANASE JRNL TITL 2 FROM AN ACHATINA FULICA GUT METAGENOMIC LIBRARY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 14890 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 + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 733 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2513 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 51 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.80 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.380 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5CZL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212423. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-15 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 : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.458 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14898 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.390 REMARK 200 RESOLUTION RANGE LOW (A) : 44.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.15900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.76100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.380 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG1000 10% PEG8000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 25.21200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.83150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.18700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.83150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.21200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.18700 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: 300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 VAL A 2 REMARK 465 ARG A 318 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 31 76.77 -117.69 REMARK 500 LEU A 74 -157.44 -101.95 REMARK 500 VAL A 82 50.24 -107.92 REMARK 500 ALA A 136 -134.74 54.93 REMARK 500 ARG A 150 -89.89 -96.24 REMARK 500 ASN A 151 -84.29 -144.11 REMARK 500 SER A 223 -118.05 -132.13 REMARK 500 ASP A 237 102.36 -166.11 REMARK 500 ASP A 316 28.41 -75.30 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 PO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 402 DBREF 5CZL A -19 318 PDB 5CZL 5CZL -19 318 SEQRES 1 A 338 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 338 LEU VAL PRO ARG GLY SER HIS MET VAL LEU PRO ARG ALA SEQRES 3 A 338 TRP ALA ASP THR ALA TRP GLU SER TYR LYS SER ARG PHE SEQRES 4 A 338 MET MET ALA ASP GLY ARG ILE VAL ASP THR GLY ASN GLY SEQRES 5 A 338 SER VAL SER HIS THR GLU GLY GLN GLY PHE ALA MET LEU SEQRES 6 A 338 LEU ALA VAL ALA LYS ASN ASP ARG PRO ALA PHE ASP LYS SEQRES 7 A 338 LEU TRP GLN TRP THR ASP LYS THR LEU ARG ASN LYS ASP SEQRES 8 A 338 ASN GLY LEU PHE TYR TRP ARG TYR ASN PRO VAL ALA PRO SEQRES 9 A 338 ASP PRO ILE ALA ASP LYS ASN ASP ALA THR ASP GLY ASP SEQRES 10 A 338 THR LEU ILE ALA TRP ALA LEU LEU ARG ALA GLN GLN GLN SEQRES 11 A 338 TRP GLY ASP LYS SER TYR GLY ILE ALA SER ASP ALA ILE SEQRES 12 A 338 THR ALA SER LEU LEU LYS SER THR VAL ILE THR PHE ALA SEQRES 13 A 338 GLY HIS GLN VAL MET LEU PRO GLY ALA LYS GLY PHE ASN SEQRES 14 A 338 ARG ASN ASP HIS VAL ASN LEU ASN PRO SER TYR PHE ILE SEQRES 15 A 338 PHE PRO ALA TRP GLN ALA PHE ALA ALA ARG THR HIS LEU SEQRES 16 A 338 THR ALA TRP ARG LYS LEU GLN SER ASP GLY LYS ALA LEU SEQRES 17 A 338 LEU GLY LYS MET ALA TRP GLY LYS ALA GLN LEU PRO SER SEQRES 18 A 338 ASP TRP VAL ALA LEU ARG ALA ASP GLY ARG MET GLU PRO SEQRES 19 A 338 ALA LYS GLU TRP PRO PRO ARG MET SER TYR ASP ALA ILE SEQRES 20 A 338 ARG ILE PRO LEU TYR LEU SER TRP ALA ASP PRO GLN SER SEQRES 21 A 338 ALA LEU LEU THR PRO TRP LYS SER TRP PHE GLN SER TYR SEQRES 22 A 338 PRO ARG LEU GLN THR PRO ALA TRP VAL ASN VAL ASN THR SEQRES 23 A 338 ASN ASP VAL ALA PRO TRP PHE MET THR GLY GLY LEU LEU SEQRES 24 A 338 ALA VAL ARG ASP LEU THR THR GLY GLU ALA GLN ASP ASP SEQRES 25 A 338 PRO GLN LEU SER ALA GLN ASP ASP TYR TYR SER ALA SER SEQRES 26 A 338 LEU LYS MET LEU VAL TRP LEU ALA LYS ASN ASP ARG ARG HET PO4 A 401 5 HET PO4 A 402 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 2(O4 P 3-) FORMUL 4 HOH *51(H2 O) HELIX 1 AA1 THR A 10 MET A 20 1 11 HELIX 2 AA2 THR A 37 LYS A 50 1 14 HELIX 3 AA3 ASP A 52 ARG A 68 1 17 HELIX 4 AA4 ALA A 93 GLY A 112 1 20 HELIX 5 AA5 ASP A 113 THR A 131 1 19 HELIX 6 AA6 ASN A 157 PHE A 161 5 5 HELIX 7 AA7 ILE A 162 HIS A 174 1 13 HELIX 8 AA8 LEU A 175 MET A 192 1 18 HELIX 9 AA9 ILE A 227 ASP A 237 1 11 HELIX 10 AB1 SER A 240 LEU A 242 5 3 HELIX 11 AB2 LEU A 243 SER A 252 1 10 HELIX 12 AB3 PRO A 254 THR A 258 5 5 HELIX 13 AB4 THR A 275 GLY A 287 1 13 HELIX 14 AB5 ASP A 300 ASP A 316 1 17 SHEET 1 AA1 2 SER A 35 HIS A 36 0 SHEET 2 AA1 2 ARG A 78 TYR A 79 -1 O TYR A 79 N SER A 35 SHEET 1 AA2 2 VAL A 132 PHE A 135 0 SHEET 2 AA2 2 HIS A 138 MET A 141 -1 O VAL A 140 N ILE A 133 SHEET 1 AA3 3 HIS A 153 LEU A 156 0 SHEET 2 AA3 3 VAL A 204 ARG A 207 -1 O VAL A 204 N LEU A 156 SHEET 3 AA3 3 MET A 212 PRO A 214 -1 O GLU A 213 N ALA A 205 SHEET 1 AA4 2 ARG A 221 MET A 222 0 SHEET 2 AA4 2 VAL A 262 ASN A 263 -1 O VAL A 262 N MET A 222 SITE 1 AC1 6 HIS A 174 ARG A 179 PRO A 254 ARG A 255 SITE 2 AC1 6 HOH A 513 HOH A 514 SITE 1 AC2 2 ARG A 150 HIS A 153 CRYST1 50.424 76.374 95.663 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 0.019832 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013093 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010453 0.00000