PDB Short entry for 1OA4 HEADER HYDROLASE 28-DEC-02 1OA4 TITLE COMPARISON OF FAMILY 12 GLYCOSIDE HYDROLASES AND RECRUITED TITLE 2 SUBSTITUTIONS IMPORTANT FOR THERMAL STABILITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-BETA-1,4-GLUCANASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 32-253; COMPND 5 SYNONYM: ENDOGLUCANASE, CEL12A; COMPND 6 EC: 3.2.1.4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES SP. 11AG8; SOURCE 3 ORGANISM_TAXID: 133452; SOURCE 4 EXPRESSION_SYSTEM: STREPTOMYCES LIVIDANS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 1916 KEYWDS HYDROLASE, CELLULASE, CELLULOSE DEGRADATION, ENDOGLUCANASE, GLYCOSYL KEYWDS 2 HYDROLASE, GH FAMILY 12, STREPTOMYCES SP 11AG8 CEL12A EXPDTA X-RAY DIFFRACTION AUTHOR M.SANDGREN,P.J.GUALFETTI,A.SHAW,L.S.GROSS,M.SALDAJENO,A.G.DAY, AUTHOR 2 T.A.JONES,C.MITCHINSON REVDAT 3 13-DEC-23 1OA4 1 REMARK REVDAT 2 24-FEB-09 1OA4 1 VERSN REVDAT 1 27-MAR-03 1OA4 0 JRNL AUTH M.SANDGREN,P.J.GUALFETTI,A.SHAW,L.S.GROSS,M.SALDAJENO, JRNL AUTH 2 A.G.DAY,T.A.JONES,C.MITCHINSON JRNL TITL COMPARISON OF FAMILY 12 GLYCOSIDE HYDROLASES AND RECRUITED JRNL TITL 2 SUBSTITUTIONS IMPORTANT FOR THERMAL STABILITY JRNL REF PROTEIN SCI. V. 12 848 2003 JRNL REFN ISSN 0961-8368 JRNL PMID 12649442 JRNL DOI 10.1110/PS.0237703 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 72.1 REMARK 3 NUMBER OF REFLECTIONS : 25464 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 + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 821 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1685 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 117 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.53000 REMARK 3 B22 (A**2) : 0.59000 REMARK 3 B33 (A**2) : -1.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.082 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1OA4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-DEC-02. REMARK 100 THE DEPOSITION ID IS D_1290011925. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 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 RU200 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26559 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 29.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 73.0 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.4000 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) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.16100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1NLR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.00 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 32.58000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.29500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.31500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.29500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.58000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.31500 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: PQS 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: 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 VAL A 131 CG1 - CB - CG2 ANGL. DEV. = 10.9 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 GLN A 14 19.72 59.48 REMARK 500 ARG A 16 -31.24 -148.32 REMARK 500 THR A 35 -165.47 -100.49 REMARK 500 ALA A 44 62.77 -151.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OA2 RELATED DB: PDB REMARK 900 COMPARISON OF FAMILY 12 GLYCOSIDE HYDROLASES AND RECRUITED REMARK 900 SUBSTITUTIONS IMPORTANT FOR THERMAL STABILITY REMARK 900 RELATED ID: 1OA3 RELATED DB: PDB REMARK 900 COMPARISON OF FAMILY 12 GLYCOSIDE HYDROLASES AND RECRUITED REMARK 900 SUBSTITUTIONS IMPORTANT FOR THERMAL STABILITY DBREF 1OA4 A 1 222 UNP Q9KIH1 Q9KIH1 32 253 SEQRES 1 A 222 ASN GLN GLN ILE CYS ASP ARG TYR GLY THR THR THR ILE SEQRES 2 A 222 GLN ASP ARG TYR VAL VAL GLN ASN ASN ARG TRP GLY THR SEQRES 3 A 222 SER ALA THR GLN CYS ILE ASN VAL THR GLY ASN GLY PHE SEQRES 4 A 222 GLU ILE THR GLN ALA ASP GLY SER VAL PRO THR ASN GLY SEQRES 5 A 222 ALA PRO LYS SER TYR PRO SER VAL TYR ASP GLY CYS HIS SEQRES 6 A 222 TYR GLY ASN CYS ALA PRO ARG THR THR LEU PRO MET ARG SEQRES 7 A 222 ILE SER SER ILE GLY SER ALA PRO SER SER VAL SER TYR SEQRES 8 A 222 ARG TYR THR GLY ASN GLY VAL TYR ASN ALA ALA TYR ASP SEQRES 9 A 222 ILE TRP LEU ASP PRO THR PRO ARG THR ASN GLY VAL ASN SEQRES 10 A 222 ARG THR GLU ILE MET ILE TRP PHE ASN ARG VAL GLY PRO SEQRES 11 A 222 VAL GLN PRO ILE GLY SER PRO VAL GLY THR ALA HIS VAL SEQRES 12 A 222 GLY GLY ARG SER TRP GLU VAL TRP THR GLY SER ASN GLY SEQRES 13 A 222 SER ASN ASP VAL ILE SER PHE LEU ALA PRO SER ALA ILE SEQRES 14 A 222 SER SER TRP SER PHE ASP VAL LYS ASP PHE VAL ASP GLN SEQRES 15 A 222 ALA VAL SER HIS GLY LEU ALA THR PRO ASP TRP TYR LEU SEQRES 16 A 222 THR SER ILE GLN ALA GLY PHE GLU PRO TRP GLU GLY GLY SEQRES 17 A 222 THR GLY LEU ALA VAL ASN SER PHE SER SER ALA VAL ASN SEQRES 18 A 222 ALA FORMUL 2 HOH *117(H2 O) HELIX 1 1 SER A 80 ILE A 82 5 3 HELIX 2 2 VAL A 176 HIS A 186 1 11 SHEET 1 AA 6 GLN A 2 ILE A 4 0 SHEET 2 AA 6 GLN A 30 VAL A 34 -1 O ILE A 32 N ILE A 4 SHEET 3 AA 6 PHE A 39 ALA A 44 -1 O GLU A 40 N ASN A 33 SHEET 4 AA 6 ALA A 212 SER A 218 -1 O VAL A 213 N PHE A 39 SHEET 5 AA 6 PRO A 86 ARG A 92 -1 O SER A 88 N SER A 217 SHEET 6 AA 6 SER A 171 ASP A 175 -1 O TRP A 172 N VAL A 89 SHEET 1 AB 4 THR A 10 ILE A 13 0 SHEET 2 AB 4 TYR A 17 GLN A 20 -1 O TYR A 17 N ILE A 13 SHEET 3 AB 4 SER A 59 HIS A 65 -1 O SER A 59 N GLN A 20 SHEET 4 AB 4 TYR A 194 GLU A 206 -1 O THR A 196 N CYS A 64 SHEET 1 AC 4 THR A 10 ILE A 13 0 SHEET 2 AC 4 TYR A 17 GLN A 20 -1 O TYR A 17 N ILE A 13 SHEET 3 AC 4 SER A 59 HIS A 65 -1 O SER A 59 N GLN A 20 SHEET 4 AC 4 ASN A 68 CYS A 69 -1 O ASN A 68 N HIS A 65 SSBOND 1 CYS A 5 CYS A 31 1555 1555 2.02 SSBOND 2 CYS A 64 CYS A 69 1555 1555 2.04 CISPEP 1 LEU A 75 PRO A 76 0 0.04 CRYST1 65.160 54.630 62.590 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 0.015347 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015977 0.00000