HEADER HYDROLASE 23-NOV-05 2F4G
TITLE TRICLINIC CROSS-LINKED LYSOZYME SOAKED IN BROMOETHANOL 1M
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSOZYME C;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C, ALLERGEN GAL D 4, GAL D IV;
COMPND 5 EC: 3.2.1.17
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS;
SOURCE 3 ORGANISM_COMMON: CHICKEN;
SOURCE 4 ORGANISM_TAXID: 9031;
SOURCE 5 OTHER_DETAILS: EGG
KEYWDS DENATURATION, LYSOZYME, BARNASE, CROSS-LINKED CRYSTALS,
KEYWDS 2 GLUTARALDEHYDE, UREA, THIOUREA, BROMOETHANOL, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR T.PRANGE,M.SALEM
REVDAT 4 23-AUG-23 2F4G 1 REMARK
REVDAT 3 24-FEB-09 2F4G 1 VERSN
REVDAT 2 06-JUN-06 2F4G 1 JRNL
REVDAT 1 25-APR-06 2F4G 0
JRNL AUTH M.SALEM,Y.MAUGUEN,T.PRANGE
JRNL TITL ON THE EDGE OF THE DENATURATION PROCESS: APPLICATION OF
JRNL TITL 2 X-RAY DIFFRACTION TO BARNASE AND LYSOZYME CROSS-LINKED
JRNL TITL 3 CRYSTALS WITH DENATURANTS IN MOLAR CONCENTRATIONS.
JRNL REF BIOCHIM.BIOPHYS.ACTA V.1764 903 2006
JRNL REFN ISSN 0006-3002
JRNL PMID 16600702
JRNL DOI 10.1016/J.BBAPAP.2006.02.009
REMARK 2
REMARK 2 RESOLUTION. 1.65 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) : 1.65
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.180
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : 0.180
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) : 11237
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.178
REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 10770
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1001
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 16
REMARK 3 SOLVENT ATOMS : 68
REMARK 3
REMARK 3 MODEL REFINEMENT.
REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1085.0
REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 909.00
REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0
REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4343
REMARK 3 NUMBER OF RESTRAINTS : 4170
REMARK 3
REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK 3 BOND LENGTHS (A) : 0.008
REMARK 3 ANGLE DISTANCES (A) : 0.024
REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000
REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026
REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.041
REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.046
REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.031
REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000
REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.059
REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED: NULL
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 2F4G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-05.
REMARK 100 THE DEPOSITION ID IS D_1000035440.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-MAR-02
REMARK 200 TEMPERATURE (KELVIN) : 277.0
REMARK 200 PH : 6.00
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : LURE
REMARK 200 BEAMLINE : DW32
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.964
REMARK 200 MONOCHROMATOR : SI(111)
REMARK 200 OPTICS : SI(111) CURVATED MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10770
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.654
REMARK 200 RESOLUTION RANGE LOW (A) : 10.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80
REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7
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 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS
REMARK 200 SOFTWARE USED: SHELX
REMARK 200 STARTING MODEL: 2F2N
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 31.78
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM NITRATE AS CRYSTALLIZING AGENT
REMARK 280 CROSS-LINKED BY VAPOR DIFFUSION WITH GLUTARALDEHYDE, PROTEIN 20
REMARK 280 MG/ML, PH 6.00, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K
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 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 TYR A 20 CG - CD2 - CE2 ANGL. DEV. = -5.5 DEGREES
REMARK 500 TYR A 20 CZ - CE2 - CD2 ANGL. DEV. = 7.0 DEGREES
REMARK 500 TYR A 53 CB - CG - CD1 ANGL. DEV. = -3.6 DEGREES
REMARK 500 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 3.1 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 ASP A 101 35.96 -72.18
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 NO3 A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 203
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BRJ A 300
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2F2N RELATED DB: PDB
REMARK 900 TRICLINIC LYSOZYME CROSS-LINKED WITH GLUTARALDEHYDE
REMARK 900 RELATED ID: 2F30 RELATED DB: PDB
REMARK 900 CROSS-LINKED LYSOZYME SOAKED IN 4.5M UREA
REMARK 900 RELATED ID: 2F4A RELATED DB: PDB
REMARK 900 CROSS-LINKED LYSOZYME SOAKED IN 1.75M THIOUREA
DBREF 2F4G A 1 129 UNP P00698 LYSC_CHICK 19 147
SEQRES 1 A 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS
SEQRES 2 A 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY
SEQRES 3 A 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN
SEQRES 4 A 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP
SEQRES 5 A 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN
SEQRES 6 A 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE
SEQRES 7 A 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER
SEQRES 8 A 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY
SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY
SEQRES 10 A 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU
HET NO3 A 201 4
HET NO3 A 202 4
HET NO3 A 203 4
HET BRJ A 300 4
HETNAM NO3 NITRATE ION
HETNAM BRJ 2-BROMOETHANOL
FORMUL 2 NO3 3(N O3 1-)
FORMUL 5 BRJ C2 H5 BR O
FORMUL 6 HOH *68(H2 O)
HELIX 1 1 GLY A 4 HIS A 15 1 12
HELIX 2 2 ASN A 19 TYR A 23 5 5
HELIX 3 3 SER A 24 ASN A 37 1 14
HELIX 4 4 PRO A 79 SER A 85 5 7
HELIX 5 5 ILE A 88 ASP A 101 1 14
HELIX 6 6 ASN A 103 ALA A 107 5 5
HELIX 7 7 TRP A 108 CYS A 115 1 8
HELIX 8 8 ASP A 119 ARG A 125 5 7
SHEET 1 A 3 THR A 43 ARG A 45 0
SHEET 2 A 3 THR A 51 TYR A 53 -1 O ASP A 52 N ASN A 44
SHEET 3 A 3 ILE A 58 ASN A 59 -1 O ILE A 58 N TYR A 53
SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.03
SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.05
SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.02
SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.02
SITE 1 AC1 7 ASN A 65 ASN A 74 ASN A 77 ILE A 78
SITE 2 AC1 7 PRO A 79 ARG A 112 LYS A 116
SITE 1 AC2 6 ARG A 21 ASP A 66 PRO A 79 CYS A 80
SITE 2 AC2 6 SER A 81 HOH A 323
SITE 1 AC3 5 ARG A 5 LYS A 33 PHE A 38 TRP A 62
SITE 2 AC3 5 ARG A 73
SITE 1 AC4 5 GLN A 57 TRP A 63 ALA A 107 TRP A 108
SITE 2 AC4 5 HOH A 316
CRYST1 27.130 31.750 34.190 88.96 108.42 111.47 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 0.036860 0.014497 0.013962 0.00000
SCALE2 0.000000 0.033845 0.003761 0.00000
SCALE3 0.000000 0.000000 0.031017 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
