HEADER HYDROLASE 18-NOV-05 2F30 TITLE TRICLINIC CROSS-LINKED LYSOZYME SOAKED WITH 4.5M UREA 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 5 23-AUG-23 2F30 1 REMARK REVDAT 4 18-OCT-17 2F30 1 REMARK REVDAT 3 24-FEB-09 2F30 1 VERSN REVDAT 2 06-JUN-06 2F30 1 JRNL REVDAT 1 25-APR-06 2F30 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 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 (%) : 94.1 REMARK 3 CROSS-VALIDATION METHOD : NULL 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) : 0.169 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.156 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 533 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 11319 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.166 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.156 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 6.600 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 11189 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 : 32 REMARK 3 SOLVENT ATOMS : 122 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1086.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4459 REMARK 3 NUMBER OF RESTRAINTS : 4177 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.309 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.054 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.055 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.135 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL 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 2F30 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1000035389. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-02 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 6 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(III) 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 : 11365 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 15.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : 0.03000 REMARK 200 FOR THE DATA SET : 28.3000 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) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.19500 REMARK 200 R SYM FOR SHELL (I) : 0.18200 REMARK 200 FOR SHELL : 18.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: SFALL REMARK 200 STARTING MODEL: PDB ENTRY 2F2N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.99 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, PH 6, VAPOR REMARK 280 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 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 13 CE NZ REMARK 480 ARG A 61 NH2 REMARK 480 TRP A 62 CE3 REMARK 480 ARG A 73 NH2 REMARK 480 LYS A 97 CG CE NZ REMARK 480 SER A 100 OG REMARK 480 ASN A 103 CB CG OD1 ND2 REMARK 480 ASN A 106 OD1 REMARK 480 VAL A 109 CG1 REMARK 480 ARG A 112 NH1 NH2 REMARK 480 GLN A 121 CD OE1 REMARK 480 ARG A 125 CG REMARK 480 ARG A 128 CG CD NH1 NH2 REMARK 480 LEU A 129 C CD1 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 125 NE - CZ - NH1 ANGL. DEV. = 4.0 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 103 -28.58 -149.27 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2F2N RELATED DB: PDB REMARK 900 CROSS-LINKED NATIVE LYSOZYME DBREF 2F30 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 501 4 HET NO3 A 502 4 HET NO3 A 503 4 HET NO3 A 504 4 HET NO3 A 505 4 HET NO3 A 506 4 HET URE A 601 4 HET URE A 602 4 HETNAM NO3 NITRATE ION HETNAM URE UREA FORMUL 2 NO3 6(N O3 1-) FORMUL 8 URE 2(C H4 N2 O) FORMUL 10 HOH *122(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 2.01 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.04 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.04 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 7 ARG A 21 ASN A 65 ASP A 66 CYS A 80 SITE 2 AC2 7 SER A 81 HOH A1018 HOH A1039 SITE 1 AC3 7 ARG A 5 LYS A 33 PHE A 38 TRP A 62 SITE 2 AC3 7 ARG A 73 TRP A 123 HOH A1142 SITE 1 AC4 8 ALA A 11 ARG A 14 HIS A 15 ASP A 87 SITE 2 AC4 8 ILE A 88 THR A 89 HOH A1131 HOH A1150 SITE 1 AC5 7 SER A 24 LEU A 25 GLY A 26 GLN A 41 SITE 2 AC5 7 GLN A 121 ILE A 124 HOH A1045 SITE 1 AC6 6 TYR A 23 ARG A 45 MET A 105 ASN A 106 SITE 2 AC6 6 TRP A 111 HOH A1089 SITE 1 AC7 7 GLN A 57 ILE A 58 ASN A 59 TRP A 63 SITE 2 AC7 7 ALA A 107 TRP A 108 HOH A1087 SITE 1 AC8 4 ARG A 45 CYS A 76 ASN A 77 HOH A1106 CRYST1 27.110 31.940 34.170 88.15 108.62 111.73 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 0.036887 0.014701 0.013930 0.00000 SCALE2 0.000000 0.033704 0.003306 0.00000 SCALE3 0.000000 0.000000 0.031030 0.00000