HEADER CHITIN BINDING PROTEIN 07-SEP-11 4A02 TITLE X-RAY CRYSTALLOGRAPHIC STRUCTURE OF EFCBM33A COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITIN BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 29-194; COMPND 5 SYNONYM: EFCBM33A, CBM33; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS; SOURCE 3 ORGANISM_TAXID: 1351; SOURCE 4 STRAIN: V582; SOURCE 5 ATCC: 700802; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRSET-B KEYWDS CHITIN BINDING PROTEIN, CHITIN DEGRADATION, CHITIN OXIDATION EXPDTA X-RAY DIFFRACTION AUTHOR G.VAAJE-KOLSTAD,L.A.BOHLE,S.GASEIDNES,B.DALHUS,M.BJORAS,G.MATHIESEN, AUTHOR 2 V.G.H.EIJSINK REVDAT 4 20-DEC-23 4A02 1 REMARK REVDAT 3 21-NOV-12 4A02 1 TER REVDAT 2 08-FEB-12 4A02 1 JRNL REMARK REVDAT 1 11-JAN-12 4A02 0 JRNL AUTH G.VAAJE-KOLSTAD,L.A.BOHLE,S.GASEIDNES,B.DALHUS,M.BJORAS, JRNL AUTH 2 G.MATHIESEN,V.G.H.EIJSINK JRNL TITL CHARACTERIZATION OF THE CHITINOLYTIC MACHINERY OF JRNL TITL 2 ENTEROCOCCUS FAECALIS V583 AND HIGH RESOLUTION STRUCTURE OF JRNL TITL 3 ITS OXIDATIVE CBM33 ENZYME JRNL REF J.MOL.BIOL. V. 416 239 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22210154 JRNL DOI 10.1016/J.JMB.2011.12.033 REMARK 2 REMARK 2 RESOLUTION. 0.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.096 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.116 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 5601 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 111940 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.091 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.110 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 4816 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 96841 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1300 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 286 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 14448 REMARK 3 NUMBER OF RESTRAINTS : 17468 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.031 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.092 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.099 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.133 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.040 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.112 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4A02 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1290049515. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9334 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 112000 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 23.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05300 REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.22100 REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2BEM REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M K/NA TARTRATE, 0.1 M IMIDAZOLE REMARK 280 PH 8.0 AND 0.2 M NACL. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.76867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.88433 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2060 O HOH A 2070 2.05 REMARK 500 O HOH A 2170 O HOH A 2171 2.11 REMARK 500 O HOH A 2171 O HOH A 2175 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 29 CB HIS A 29 CG 0.136 REMARK 500 REMARK 500 REMARK: NULL 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 HIS A 29 CA - CB - CG ANGL. DEV. = -12.7 DEGREES REMARK 500 GLU A 59 OE1 - CD - OE2 ANGL. DEV. = -9.3 DEGREES REMARK 500 ARG A 115 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP A 146 CB - CG - OD1 ANGL. DEV. = 7.5 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 52 73.83 42.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2035 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH A2036 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A2044 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A2052 DISTANCE = 6.48 ANGSTROMS DBREF 4A02 A 29 194 UNP Q838S1 Q838S1_ENTFA 29 194 SEQRES 1 A 166 HIS GLY TYR VAL ALA SER PRO GLY SER ARG ALA PHE PHE SEQRES 2 A 166 GLY SER SER ALA GLY GLY ASN LEU ASN THR ASN VAL GLY SEQRES 3 A 166 ARG ALA GLN TRP GLU PRO GLN SER ILE GLU ALA PRO LYS SEQRES 4 A 166 ASN THR PHE ILE THR GLY LYS LEU ALA SER ALA GLY VAL SEQRES 5 A 166 SER GLY PHE GLU PRO LEU ASP GLU GLN THR ALA THR ARG SEQRES 6 A 166 TRP HIS LYS THR ASN ILE THR THR GLY PRO LEU ASP ILE SEQRES 7 A 166 THR TRP ASN LEU THR ALA GLN HIS ARG THR ALA SER TRP SEQRES 8 A 166 ASP TYR TYR ILE THR LYS ASN GLY TRP ASN PRO ASN GLN SEQRES 9 A 166 PRO LEU ASP ILE LYS ASN PHE ASP LYS ILE ALA SER ILE SEQRES 10 A 166 ASP GLY LYS GLN GLU VAL PRO ASN LYS VAL VAL LYS GLN SEQRES 11 A 166 THR ILE ASN ILE PRO THR ASP ARG LYS GLY TYR HIS VAL SEQRES 12 A 166 ILE TYR ALA VAL TRP GLY ILE GLY ASP THR VAL ASN ALA SEQRES 13 A 166 PHE TYR GLN ALA ILE ASP VAL ASN ILE GLN FORMUL 2 HOH *286(H2 O) HELIX 1 1 SER A 37 GLY A 42 1 6 HELIX 2 2 SER A 43 GLY A 47 5 5 HELIX 3 3 VAL A 53 TRP A 58 5 6 HELIX 4 4 PHE A 83 GLU A 88 5 6 HELIX 5 5 ASP A 135 LYS A 137 5 3 SHEET 1 AA 3 GLY A 30 SER A 34 0 SHEET 2 AA 3 GLY A 102 LEU A 110 -1 O THR A 107 N ALA A 33 SHEET 3 AA 3 VAL A 155 ILE A 162 -1 O VAL A 156 N TRP A 108 SHEET 1 AB 2 GLU A 64 PRO A 66 0 SHEET 2 AB 2 ASN A 183 ILE A 193 -1 O ALA A 184 N ALA A 65 SHEET 1 AC 2 THR A 97 ILE A 99 0 SHEET 2 AC 2 ASN A 183 ILE A 193 -1 O ASP A 190 N THR A 97 SHEET 1 AD 5 PHE A 139 GLU A 150 0 SHEET 2 AD 5 THR A 116 THR A 124 -1 O THR A 116 N GLN A 149 SHEET 3 AD 5 GLY A 168 ILE A 178 -1 O VAL A 171 N THR A 124 SHEET 4 AD 5 ASN A 183 ILE A 193 -1 O ASN A 183 N ILE A 178 SHEET 5 AD 5 THR A 97 ILE A 99 -1 O THR A 97 N ASN A 192 SHEET 1 AE 5 PHE A 139 GLU A 150 0 SHEET 2 AE 5 THR A 116 THR A 124 -1 O THR A 116 N GLN A 149 SHEET 3 AE 5 GLY A 168 ILE A 178 -1 O VAL A 171 N THR A 124 SHEET 4 AE 5 ASN A 183 ILE A 193 -1 O ASN A 183 N ILE A 178 SHEET 5 AE 5 GLU A 64 PRO A 66 -1 O ALA A 65 N ALA A 184 CISPEP 1 SER A 34 PRO A 35 0 -21.40 CRYST1 52.109 52.109 59.653 90.00 90.00 120.00 P 32 3 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 0.019191 0.011080 0.000000 0.00000 SCALE2 0.000000 0.022159 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016764 0.00000