10 20 30 40 50 60 70 80 4ENG - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER GLYCOSYL HYDROLASE 17-OCT-96 4ENG
TITLE STRUCTURE OF ENDOGLUCANASE V CELLOHEXAOSE COMPLEX
COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOGLUCANASE V CELLOHEXAOSE COMPLEX; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC CORE, RESIDUES 1 - 210; COMPND 5 EC: 3.2.1.4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMICOLA INSOLENS; SOURCE 3 ORGANISM_TAXID: 34413
KEYWDS HYDROLASE, ENDOGLUCANASE, GLYCOSYL HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR G.J.DAVIES,M.SCHULEIN
REVDAT 3 13-JUL-11 4ENG 1 VERSN REVDAT 2 24-FEB-09 4ENG 1 VERSN REVDAT 1 16-JUN-97 4ENG 0
JRNL AUTH G.J.DAVIES,G.DODSON,M.H.MOORE,S.P.TOLLEY,Z.DAUTER, JRNL AUTH 2 K.S.WILSON,G.RASMUSSEN,M.SCHULEIN JRNL TITL STRUCTURE DETERMINATION AND REFINEMENT OF THE HUMICOLA JRNL TITL 2 INSOLENS ENDOGLUCANASE V AT 1.5 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 52 7 1996 JRNL REFN ISSN 0907-4449 JRNL PMID 15299721 JRNL DOI 10.1107/S0907444995009280
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.J.DAVIES,S.P.TOLLEY,B.HENRISSAT,C.HJORT,M.SCHULEIN REMARK 1 TITL STRUCTURES OF OLIGOSACCHARIDE-BOUND FORMS OF THE REMARK 1 TITL 2 ENDOGLUCANASE V FROM HUMICOLA INSOLENS AT 1.9 A RESOLUTION REMARK 1 REF BIOCHEMISTRY V. 34 16210 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH G.J.DAVIES,G.G.DODSON,R.E.HUBBARD,S.P.TOLLEY,Z.DAUTER, REMARK 1 AUTH 2 K.S.WILSON,C.HJORT,J.M.MIKKELSEN,G.RASMUSSEN,M.SCHULEIN REMARK 1 TITL STRUCTURE AND FUNCTION OF ENDOGLUCANASE V REMARK 1 REF NATURE V. 365 362 1993 REMARK 1 REFN ISSN 0028-0836
REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13406 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1581 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 132 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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): NULL 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) : 0.009 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.028 ; 0.051 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.032 ; 0.053 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.007 ; 0.016 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.110 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.164 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.245 ; 0.300 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) : 3.800 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 17.100; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 24.900; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.680 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.261 ; 5.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.184 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.506 ; 6.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 4ENG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 1993 REMARK 200 TEMPERATURE (KELVIN) : 393 REMARK 200 PH : 8.0 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (ROTAVATA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13502 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -999.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.15700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.480 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2ENG REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MG/ML ENZYME IN 20MM TRIS-HCL BUFFER REMARK 280 PH 8.0. PRECIPITANT 18%(W/V) PEG 8K. CO-CRYSTALLISED WITH 5MM REMARK 280 CELLOHEXAOSE
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 25.99000 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 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 400 REMARK 400 COMPOUND REMARK 400 THIS IS AN INACTIVE MUTANT (D10N) COMPLEX WITH THE REMARK 400 SUBSTRATE CELLOHEXAOSE. TWO HALF CELLOHEXAOSES ARE PRESENT REMARK 400 IN THE ENZYME'S -4, -3, -2 AND +1, +2 AND +3 SUBSITES. REMARK 400 REMARK 400 ENDOGLUCANASE V IS FROM GLYCOSYL HYDROLASE FAMILY 45.
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 ASP A 58 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 TYR A 168 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 196 CD - NE - CZ ANGL. DEV. = 20.9 DEGREES REMARK 500 ARG A 196 NE - CZ - NH1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 196 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 200 CD - NE - CZ ANGL. DEV. = 13.5 DEGREES REMARK 500 ARG A 200 NE - CZ - NH1 ANGL. DEV. = 8.4 DEGREES REMARK 500 ARG A 200 NE - CZ - NH2 ANGL. DEV. = -4.9 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 TRP A 9 106.78 -160.35 REMARK 500 CYS A 11 -0.19 70.10 REMARK 500 SER A 80 -164.78 -125.26 REMARK 500 SER A 110 -169.07 -177.63 REMARK 500 PHE A 139 15.17 -147.55 REMARK 500 ASP A 172 -79.55 -90.60 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 CTR A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CTR A 212
DBREF 4ENG A 1 210 UNP P43316 GUN5_HUMIN 1 210
SEQADV 4ENG ASN A 10 UNP P43316 ASP 10 ENGINEERED
SEQRES 1 A 210 ALA ASP GLY ARG SER THR ARG TYR TRP ASN CYS CYS LYS SEQRES 2 A 210 PRO SER CYS GLY TRP ALA LYS LYS ALA PRO VAL ASN GLN SEQRES 3 A 210 PRO VAL PHE SER CYS ASN ALA ASN PHE GLN ARG ILE THR SEQRES 4 A 210 ASP PHE ASP ALA LYS SER GLY CYS GLU PRO GLY GLY VAL SEQRES 5 A 210 ALA TYR SER CYS ALA ASP GLN THR PRO TRP ALA VAL ASN SEQRES 6 A 210 ASP ASP PHE ALA LEU GLY PHE ALA ALA THR SER ILE ALA SEQRES 7 A 210 GLY SER ASN GLU ALA GLY TRP CYS CYS ALA CYS TYR GLU SEQRES 8 A 210 LEU THR PHE THR SER GLY PRO VAL ALA GLY LYS LYS MET SEQRES 9 A 210 VAL VAL GLN SER THR SER THR GLY GLY ASP LEU GLY SER SEQRES 10 A 210 ASN HIS PHE ASP LEU ASN ILE PRO GLY GLY GLY VAL GLY SEQRES 11 A 210 ILE PHE ASP GLY CYS THR PRO GLN PHE GLY GLY LEU PRO SEQRES 12 A 210 GLY GLN ARG TYR GLY GLY ILE SER SER ARG ASN GLU CYS SEQRES 13 A 210 ASP ARG PHE PRO ASP ALA LEU LYS PRO GLY CYS TYR TRP SEQRES 14 A 210 ARG PHE ASP TRP PHE LYS ASN ALA ASP ASN PRO SER PHE SEQRES 15 A 210 SER PHE ARG GLN VAL GLN CYS PRO ALA GLU LEU VAL ALA SEQRES 16 A 210 ARG THR GLY CYS ARG ARG ASN ASP ASP GLY ASN PHE PRO SEQRES 17 A 210 ALA VAL
HET CTR A 211 34 HET CTR A 212 34
HETNAM CTR CELLOTRIOSE
HETSYN CTR DEXTRIN
FORMUL 2 CTR 2(C18 H32 O16) FORMUL 4 HOH *132(H2 O)
HELIX 1 1 SER A 15 GLY A 17 5 3 HELIX 2 2 GLU A 82 TRP A 85 1 4 HELIX 3 3 GLY A 134 PHE A 139 1 6 HELIX 4 4 ARG A 153 ARG A 158 5 6 HELIX 5 5 ASP A 161 PHE A 171 1 11 HELIX 6 6 ALA A 191 THR A 197 1 7 HELIX 7 7 ASP A 204 ASN A 206 5 3
SHEET 1 A 6 ARG A 4 TYR A 8 0 SHEET 2 A 6 HIS A 119 ASN A 123 1 N PHE A 120 O ARG A 4 SHEET 3 A 6 PHE A 68 SER A 76 -1 N SER A 76 O HIS A 119 SHEET 4 A 6 LYS A 103 SER A 110 1 N LYS A 103 O ALA A 69 SHEET 5 A 6 CYS A 89 PHE A 94 -1 N LEU A 92 O MET A 104 SHEET 6 A 6 PHE A 182 VAL A 187 -1 N VAL A 187 O CYS A 89 SHEET 1 B 2 TRP A 62 ASN A 65 0 SHEET 2 B 2 PHE A 68 LEU A 70 -1 N LEU A 70 O TRP A 62
SSBOND 1 CYS A 11 CYS A 135 1555 1555 2.05 SSBOND 2 CYS A 12 CYS A 47 1555 1555 2.00 SSBOND 3 CYS A 16 CYS A 86 1555 1555 2.03 SSBOND 4 CYS A 31 CYS A 56 1555 1555 2.05 SSBOND 5 CYS A 87 CYS A 199 1555 1555 2.02 SSBOND 6 CYS A 89 CYS A 189 1555 1555 2.03 SSBOND 7 CYS A 156 CYS A 167 1555 1555 2.02
SITE 1 AC1 19 ASN A 10 CYS A 12 LYS A 13 SER A 15 SITE 2 AC1 19 TRP A 18 LYS A 21 SER A 45 THR A 111 SITE 3 AC1 19 PHE A 132 HOH A 287 HOH A 289 HOH A 292 SITE 4 AC1 19 HOH A 293 HOH A 294 HOH A 302 HOH A 303 SITE 5 AC1 19 HOH A 308 HOH A 311 HOH A 344 SITE 1 AC2 15 THR A 6 ARG A 7 TYR A 8 ASP A 114 SITE 2 AC2 15 ASP A 121 GLY A 127 GLY A 128 VAL A 129 SITE 3 AC2 15 GLY A 130 TYR A 147 GLY A 148 ASP A 178 SITE 4 AC2 15 ASN A 179 HOH A 309 HOH A 312
CRYST1 41.930 51.980 42.010 90.00 97.73 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 0.023849 0.000000 0.003237 0.00000
SCALE2 0.000000 0.019238 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024022 0.00000