HEADER HYDROLASE (GLUCANASE) 25-AUG-95 1GBG TITLE BACILLUS LICHENIFORMIS BETA-GLUCANASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: (1,3-1,4)-BETA-D-GLUCAN 4 GLUCANOHYDROLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-GLUCANASE, LICHENASE; COMPND 5 EC: 3.2.1.73; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LICHENIFORMIS; SOURCE 3 ORGANISM_TAXID: 1402; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PBR328 KEYWDS HYDROLASE (GLUCANASE) EXPDTA X-RAY DIFFRACTION AUTHOR M.HAHN,U.HEINEMANN REVDAT 2 24-FEB-09 1GBG 1 VERSN REVDAT 1 07-DEC-95 1GBG 0 JRNL AUTH M.HAHN,J.PONS,A.PLANAS,E.QUEROL,U.HEINEMANN JRNL TITL CRYSTAL STRUCTURE OF BACILLUS LICHENIFORMIS JRNL TITL 2 1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE AT 1.8 A JRNL TITL 3 RESOLUTION. JRNL REF FEBS LETT. V. 374 221 1995 JRNL REFN ISSN 0014-5793 JRNL PMID 7589539 JRNL DOI 10.1016/0014-5793(95)01111-Q REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.KEITEL,O.SIMON,R.BORRISS,U.HEINEMANN REMARK 1 TITL MOLECULAR AND ACTIVE-SITE STRUCTURE OF A BACILLUS REMARK 1 TITL 2 1,3-1,4-BETA-GLUCANASE REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 90 5287 1993 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.LLOBERAS,J.A.PEREZ-PONS,E.QUEROL REMARK 1 TITL MOLECULAR CLONING, EXPRESSION AND NUCLEOTIDE REMARK 1 TITL 2 SEQUENCE OF THE ENDO-BETA-1,3-1,4-D-GLUCANASE GENE REMARK 1 TITL 3 FROM BACILLUS LICHENIFORMIS REMARK 1 REF EUR.J.BIOCHEM. V. 197 337 1991 REMARK 1 REFN ISSN 0014-2956 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 16792 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1724 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.004 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 1.800 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : 26.090; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.006 ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : 0.005 ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : 16.000; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ASN 28 IS IN CONTACT WITH A REMARK 3 NEIGHBORING MOLECULE. THEREFORE ITS DIHEDRAL ANGLES LIE REMARK 3 OUTSIDE THE EXPECTED RANGE. REMARK 4 REMARK 4 1GBG 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 : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, MADNES REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 BOND LENGTHS OF SIDE CHAINS OF GLU AND ASP FOLLOW THE TNT REMARK 400 STANDARD FOR PROTONATED CARBOXY GROUPS. 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 150 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 150 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 161 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 190 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 190 CB - CG - OD2 ANGL. DEV. = -6.3 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 ASN A 28 -117.83 44.48 REMARK 500 ASN A 31 48.61 -102.29 REMARK 500 ASN A 84 139.27 178.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASN A 28 22.9 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL 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 CA A 373 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 9 O REMARK 620 2 GLY A 45 O 87.5 REMARK 620 3 ASN A 207 O 75.9 95.9 REMARK 620 4 ASN A 207 OD1 147.0 93.8 71.2 REMARK 620 5 HOH A 287 O 128.7 80.6 154.6 83.9 REMARK 620 6 HOH A 289 O 66.9 80.2 142.7 145.8 62.0 REMARK 620 7 HOH A 359 O 88.1 167.8 94.1 96.1 93.3 87.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CA1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 373 DBREF 1GBG A 1 214 UNP P27051 GUB_BACLI 30 243 SEQADV 1GBG TYR A 203 UNP P27051 SER 232 CONFLICT SEQADV 1GBG ALA A 204 UNP P27051 ARG 233 CONFLICT SEQADV 1GBG HIS A 205 UNP P27051 SER 234 CONFLICT SEQADV 1GBG TYR A 206 UNP P27051 LEU 235 CONFLICT SEQADV 1GBG ASN A 207 UNP P27051 HIS 236 CONFLICT SEQRES 1 A 214 GLN THR GLY GLY SER PHE TYR GLU PRO PHE ASN ASN TYR SEQRES 2 A 214 ASN THR GLY LEU TRP GLN LYS ALA ASP GLY TYR SER ASN SEQRES 3 A 214 GLY ASN MET PHE ASN CYS THR TRP ARG ALA ASN ASN VAL SEQRES 4 A 214 SER MET THR SER LEU GLY GLU MET ARG LEU SER LEU THR SEQRES 5 A 214 SER PRO SER TYR ASN LYS PHE ASP CYS GLY GLU ASN ARG SEQRES 6 A 214 SER VAL GLN THR TYR GLY TYR GLY LEU TYR GLU VAL ASN SEQRES 7 A 214 MET LYS PRO ALA LYS ASN VAL GLY ILE VAL SER SER PHE SEQRES 8 A 214 PHE THR TYR THR GLY PRO THR ASP GLY THR PRO TRP ASP SEQRES 9 A 214 GLU ILE ASP ILE GLU PHE LEU GLY LYS ASP THR THR LYS SEQRES 10 A 214 VAL GLN PHE ASN TYR TYR THR ASN GLY VAL GLY ASN HIS SEQRES 11 A 214 GLU LYS ILE VAL ASN LEU GLY PHE ASP ALA ALA ASN SER SEQRES 12 A 214 TYR HIS THR TYR ALA PHE ASP TRP GLN PRO ASN SER ILE SEQRES 13 A 214 LYS TRP TYR VAL ASP GLY GLN LEU LYS HIS THR ALA THR SEQRES 14 A 214 THR GLN ILE PRO GLN THR PRO GLY LYS ILE MET MET ASN SEQRES 15 A 214 LEU TRP ASN GLY ALA GLY VAL ASP GLU TRP LEU GLY SER SEQRES 16 A 214 TYR ASN GLY VAL THR PRO LEU TYR ALA HIS TYR ASN TRP SEQRES 17 A 214 VAL ARG TYR THR LYS ARG HET CA A 373 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *158(H2 O) HELIX 1 1 ALA A 36 ASN A 38 5 3 HELIX 2 2 PRO A 97 ASP A 99 5 3 HELIX 3 3 ASP A 190 LEU A 193 1 4 SHEET 1 A 6 PHE A 6 GLU A 8 0 SHEET 2 A 6 HIS A 205 LYS A 213 -1 N TYR A 211 O PHE A 6 SHEET 3 A 6 GLY A 73 LYS A 80 -1 N LYS A 80 O HIS A 205 SHEET 4 A 6 HIS A 145 GLN A 152 -1 N TRP A 151 O GLY A 73 SHEET 5 A 6 SER A 155 VAL A 160 -1 N TYR A 159 O ALA A 148 SHEET 6 A 6 GLN A 163 ALA A 168 -1 N ALA A 168 O ILE A 156 SHEET 1 B 7 TRP A 18 LYS A 20 0 SHEET 2 B 7 GLY A 62 SER A 66 -1 N ARG A 65 O GLN A 19 SHEET 3 B 7 LYS A 178 ASN A 185 -1 N LEU A 183 O GLY A 62 SHEET 4 B 7 ILE A 87 THR A 95 -1 N TYR A 94 O LYS A 178 SHEET 5 B 7 ASP A 104 LEU A 111 -1 N PHE A 110 O SER A 89 SHEET 6 B 7 LYS A 117 TYR A 123 -1 N TYR A 123 O GLU A 105 SHEET 7 B 7 LYS A 132 ASN A 135 -1 N VAL A 134 O VAL A 118 SHEET 1 C 3 VAL A 39 MET A 41 0 SHEET 2 C 3 MET A 47 LEU A 51 -1 N ARG A 48 O SER A 40 SHEET 3 C 3 LEU A 202 TYR A 206 -1 N TYR A 206 O MET A 47 SSBOND 1 CYS A 32 CYS A 61 1555 1555 2.06 LINK CA CA A 373 O PRO A 9 1555 1555 2.57 LINK CA CA A 373 O GLY A 45 1555 1555 2.56 LINK CA CA A 373 O ASN A 207 1555 1555 2.66 LINK CA CA A 373 OD1 ASN A 207 1555 1555 2.66 LINK CA CA A 373 O HOH A 287 1555 1555 2.59 LINK CA CA A 373 O HOH A 289 1555 1555 2.84 LINK CA CA A 373 O HOH A 359 1555 1655 2.89 CISPEP 1 THR A 200 PRO A 201 0 -0.32 SITE 1 CA1 6 PRO A 9 GLY A 45 ASN A 207 HOH A 216 SITE 2 CA1 6 HOH A 217 HOH A 218 SITE 1 AC1 6 PRO A 9 GLY A 45 ASN A 207 HOH A 287 SITE 2 AC1 6 HOH A 289 HOH A 359 CRYST1 35.330 39.130 43.880 64.66 105.86 110.68 P 1 1 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 0.028305 0.010684 0.004417 0.00000 SCALE2 0.000000 0.027316 -0.010822 0.00000 SCALE3 0.000000 0.000000 0.025483 0.00000