10 20 30 40 50 60 70 80 3ENG - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER GLYCOSYL HYDROLASE 17-OCT-96 3ENG
TITLE STRUCTURE OF ENDOGLUCANASE V CELLOBIOSE COMPLEX
COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOGLUCANASE V CELLOBIOSE COMPLEX; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC CORE, RESIDUES 1 - 210; COMPND 5 EC: 3.2.1.4
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 2 24-FEB-09 3ENG 1 VERSN REVDAT 1 16-JUN-97 3ENG 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 JRNL TITL 2 HUMICOLA INSOLENS ENDOGLUCANASE V AT 1.5 A JRNL TITL 3 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, REMARK 1 AUTH 2 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 REMARK 1 TITL 3 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, REMARK 1 AUTH 2 Z.DAUTER,K.S.WILSON,C.HJORT,J.M.MIKKELSEN, REMARK 1 AUTH 3 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 : 13070 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) : 0.145 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 : 1605 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 152 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 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.032 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.008 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.119 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.161 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.255 ; 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) : 16.700; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 24.600; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.621 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.174 ; 5.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.945 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.413 ; 6.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THIS IS A COMPLEX WITH THE PRODUCT REMARK 3 CELLOBIOSE. THIS IS BOUND IN THE +1 AND +2 SUBSITES OF THE REMARK 3 ENZYME. THESE ARE LABELLED AS THE E AND F RESIDUES OF REMARK 3 CELLOBIOSE. IT WAS SOLVED BY MOLECULAR REPLACEMENT USING THE REMARK 3 NATIVE EGV STRUCTURE DESCRIBED IN REFERENCE 1 (ABOVE)
REMARK 4 REMARK 4 3ENG 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 : 13151 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 (%) : 96.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.5000 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 (%) : 78.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.11800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.440 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 (%): 35.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MG/ML ENZYME IN 20MM TRIS-HCL REMARK 280 BUFFER PH 8.0. PRECIPITANT 18%(W/V) PEG 8K. CO-CRYSTALLISED REMARK 280 WITH 5MM CELLOBIOSE
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 28.09000 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 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 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 37 NE - CZ - NH2 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 158 CD - NE - CZ ANGL. DEV. = 18.3 DEGREES REMARK 500 ARG A 196 CD - NE - CZ ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG A 196 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 196 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 200 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG A 200 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 200 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 201 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP A 204 CB - CG - OD1 ANGL. DEV. = 6.6 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 9 101.10 -164.58 REMARK 500 GLN A 59 58.53 -95.38 REMARK 500 ASP A 114 78.74 -113.35 REMARK 500 ASP A 172 -79.92 -85.20 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 CBI A 214
DBREF 3ENG A 1 213 UNP P43316 GUN5_HUMIN 1 213
SEQRES 1 A 213 ALA ASP GLY ARG SER THR ARG TYR TRP ASP CYS CYS LYS SEQRES 2 A 213 PRO SER CYS GLY TRP ALA LYS LYS ALA PRO VAL ASN GLN SEQRES 3 A 213 PRO VAL PHE SER CYS ASN ALA ASN PHE GLN ARG ILE THR SEQRES 4 A 213 ASP PHE ASP ALA LYS SER GLY CYS GLU PRO GLY GLY VAL SEQRES 5 A 213 ALA TYR SER CYS ALA ASP GLN THR PRO TRP ALA VAL ASN SEQRES 6 A 213 ASP ASP PHE ALA LEU GLY PHE ALA ALA THR SER ILE ALA SEQRES 7 A 213 GLY SER ASN GLU ALA GLY TRP CYS CYS ALA CYS TYR GLU SEQRES 8 A 213 LEU THR PHE THR SER GLY PRO VAL ALA GLY LYS LYS MET SEQRES 9 A 213 VAL VAL GLN SER THR SER THR GLY GLY ASP LEU GLY SER SEQRES 10 A 213 ASN HIS PHE ASP LEU ASN ILE PRO GLY GLY GLY VAL GLY SEQRES 11 A 213 ILE PHE ASP GLY CYS THR PRO GLN PHE GLY GLY LEU PRO SEQRES 12 A 213 GLY GLN ARG TYR GLY GLY ILE SER SER ARG ASN GLU CYS SEQRES 13 A 213 ASP ARG PHE PRO ASP ALA LEU LYS PRO GLY CYS TYR TRP SEQRES 14 A 213 ARG PHE ASP TRP PHE LYS ASN ALA ASP ASN PRO SER PHE SEQRES 15 A 213 SER PHE ARG GLN VAL GLN CYS PRO ALA GLU LEU VAL ALA SEQRES 16 A 213 ARG THR GLY CYS ARG ARG ASN ASP ASP GLY ASN PHE PRO SEQRES 17 A 213 ALA VAL GLN ILE PRO
HET CBI A 214 23
HETNAM CBI CELLOBIOSE
FORMUL 2 CBI C12 H22 O11 FORMUL 3 HOH *145(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 97 VAL A 99 5 3 HELIX 4 4 GLY A 134 PHE A 139 1 6 HELIX 5 5 ARG A 153 ARG A 158 5 6 HELIX 6 6 ASP A 161 PHE A 171 1 11 HELIX 7 7 ALA A 191 THR A 197 1 7 HELIX 8 8 ASP A 204 ASN A 206 5 3
SHEET 1 A 7 SER A 181 SER A 183 0 SHEET 2 A 7 ASP A 2 TYR A 8 -1 N GLY A 3 O PHE A 182 SHEET 3 A 7 HIS A 119 ASN A 123 1 N PHE A 120 O ARG A 4 SHEET 4 A 7 PHE A 68 SER A 76 -1 N SER A 76 O HIS A 119 SHEET 5 A 7 LYS A 103 SER A 110 1 N LYS A 103 O ALA A 69 SHEET 6 A 7 CYS A 89 PHE A 94 -1 N LEU A 92 O MET A 104 SHEET 7 A 7 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 2.01 SSBOND 2 CYS A 12 CYS A 47 1555 1555 2.03 SSBOND 3 CYS A 16 CYS A 86 1555 1555 2.02 SSBOND 4 CYS A 31 CYS A 56 1555 1555 2.02 SSBOND 5 CYS A 87 CYS A 199 1555 1555 2.03 SSBOND 6 CYS A 89 CYS A 189 1555 1555 2.04 SSBOND 7 CYS A 156 CYS A 167 1555 1555 2.01
SITE 1 AC1 13 THR A 6 ARG A 7 TYR A 8 ASP A 121 SITE 2 AC1 13 GLY A 127 GLY A 128 VAL A 129 GLY A 130 SITE 3 AC1 13 TYR A 147 GLY A 148 ASN A 179 HOH A 314 SITE 4 AC1 13 HOH A 324
CRYST1 41.750 56.180 37.370 90.00 93.40 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 0.023952 0.000000 0.001423 0.00000
SCALE2 0.000000 0.017800 0.000000 0.00000
SCALE3 0.000000 0.000000 0.026807 0.00000