10 20 30 40 50 60 70 80 1C6H - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 21-DEC-99 1C6H
TITLE T4 LYSOZYME MUTANT C54T/C97A/L99A IN THE PRESENCE OF 4 ATM TITLE 2 XENON
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (LYSOZYME); COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.17; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 3 ORGANISM_TAXID: 10665; SOURCE 4 GENE: GENE E; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PHS1403
KEYWDS HYDROLASE (O-GLYCOSYL), T4 LYSOZYME, NOBLE GAS BINDING
EXPDTA X-RAY DIFFRACTION
AUTHOR M.L.QUILLIN,B.W.MATTHEWS
REVDAT 3 24-FEB-09 1C6H 1 VERSN REVDAT 2 01-APR-03 1C6H 1 JRNL REVDAT 1 04-OCT-00 1C6H 0
JRNL AUTH M.L.QUILLIN,W.A.BREYER,I.J.GRISWOLD,B.W.MATTHEWS JRNL TITL SIZE VERSUS POLARIZABILITY IN PROTEIN-LIGAND JRNL TITL 2 INTERACTIONS: BINDING OF NOBLE GASES WITHIN JRNL TITL 3 ENGINEERED CAVITIES IN PHAGE T4 LYSOZYME. JRNL REF J.MOL.BIOL. V. 302 955 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10993735 JRNL DOI 10.1006/JMBI.2000.4063
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.E.ERIKSSON,W.A.BAASE,X.-J.ZHANG,D.W.HEINZ, REMARK 1 AUTH 2 M.BLABER,E.P.BALDWIN,B.W.MATTHEWS REMARK 1 TITL RESPONSE OF A PROTEIN STRUCTURE TO CAVITY-CREATING REMARK 1 TITL 2 MUTATIONS AND ITS RELATION TO THE HYDROPHOBIC REMARK 1 TITL 3 EFFECT REMARK 1 REF SCIENCE V. 255 178 1992 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.H.WEAVER,B.W.MATTHEWS REMARK 1 TITL STRUCTURE OF BACTERIOPHAGE T4 LYSOZYME REFINED AT REMARK 1 TITL 2 1.7 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 193 189 1987 REMARK 1 REFN ISSN 0022-2836
REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT V. 5-E REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 16610 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) : NULL REMARK 3 R VALUE (WORKING SET) : NULL 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 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1650 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) : 16610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1289 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 145 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) : 0.019 ; 0.800 ; 1320 REMARK 3 BOND ANGLES (DEGREES) : 2.650 ; 1.300 ; 1770 REMARK 3 TORSION ANGLES (DEGREES) : 14.130; 0.000 ; 803 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.012 ; 2.000 ; 34 REMARK 3 GENERAL PLANES (A) : 0.016 ; 5.000 ; 189 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 2.628 ; 1.000 ; 1320 REMARK 3 NON-BONDED CONTACTS (A) : 0.028 ; 10.000; 9 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : MOEWS AND KRETSINGER REMARK 3 KSOL : 0.97 REMARK 3 BSOL : 399.60 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1C6H COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-DEC-99. REMARK 100 THE RCSB ID CODE IS RCSB001397.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-95 REMARK 200 TEMPERATURE (KELVIN) : 273.0 REMARK 200 PH : 6.9-7 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16033 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 3.010 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.9000 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) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23800 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: NULL REMARK 200 SOFTWARE USED: TNT REMARK 200 STARTING MODEL: 1L90 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8-2.2 M NAH2/K2HPO4, PH 6.9-7.1, REMARK 280 50 MM BETA-MERCAPTOETHANOL AND/OR 50 MM HYDROXYETHYL DISULFIDE
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 65.05533 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 32.52767 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.52767 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 65.05533 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN A 163 REMARK 465 LEU A 164
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 173 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 178 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 500 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 501 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 502 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 901 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 902 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 903
DBREF 1C6H A 1 164 UNP P00720 LYCV_BPT4 1 164
SEQADV 1C6H THR A 54 UNP P00720 CYS 54 ENGINEERED SEQADV 1C6H ALA A 97 UNP P00720 CYS 97 ENGINEERED SEQADV 1C6H ALA A 99 UNP P00720 LEU 99 ENGINEERED
SEQRES 1 A 164 MET ASN ILE PHE GLU MET LEU ARG ILE ASP GLU GLY LEU SEQRES 2 A 164 ARG LEU LYS ILE TYR LYS ASP THR GLU GLY TYR TYR THR SEQRES 3 A 164 ILE GLY ILE GLY HIS LEU LEU THR LYS SER PRO SER LEU SEQRES 4 A 164 ASN ALA ALA LYS SER GLU LEU ASP LYS ALA ILE GLY ARG SEQRES 5 A 164 ASN THR ASN GLY VAL ILE THR LYS ASP GLU ALA GLU LYS SEQRES 6 A 164 LEU PHE ASN GLN ASP VAL ASP ALA ALA VAL ARG GLY ILE SEQRES 7 A 164 LEU ARG ASN ALA LYS LEU LYS PRO VAL TYR ASP SER LEU SEQRES 8 A 164 ASP ALA VAL ARG ARG ALA ALA ALA ILE ASN MET VAL PHE SEQRES 9 A 164 GLN MET GLY GLU THR GLY VAL ALA GLY PHE THR ASN SER SEQRES 10 A 164 LEU ARG MET LEU GLN GLN LYS ARG TRP ASP GLU ALA ALA SEQRES 11 A 164 VAL ASN LEU ALA LYS SER ARG TRP TYR ASN GLN THR PRO SEQRES 12 A 164 ASN ARG ALA LYS ARG VAL ILE THR THR PHE ARG THR GLY SEQRES 13 A 164 THR TRP ASP ALA TYR LYS ASN LEU
HET CL A 173 1 HET CL A 178 1 HET XE A 500 1 HET XE A 501 1 HET XE A 502 1 HET BME A 901 4 HET BME A 902 4 HET BME A 903 4
HETNAM CL CHLORIDE ION HETNAM XE XENON HETNAM BME BETA-MERCAPTOETHANOL
FORMUL 2 CL 2(CL 1-) FORMUL 4 XE 3(XE) FORMUL 7 BME 3(C2 H6 O S) FORMUL 10 HOH *145(H2 O)
HELIX 1 1 ASN A 2 GLY A 12 1 11 HELIX 2 2 SER A 38 GLY A 51 1 14 HELIX 3 3 THR A 59 ASN A 81 1 23 HELIX 4 4 LEU A 84 LEU A 91 1 8 HELIX 5 5 ASP A 92 GLY A 107 1 16 HELIX 6 6 MET A 106 GLY A 113 1 8 HELIX 7 7 PHE A 114 GLN A 123 1 10 HELIX 8 8 ARG A 125 LYS A 135 1 11 HELIX 9 9 SER A 136 THR A 142 1 7 HELIX 10 10 THR A 142 GLY A 156 1 15 HELIX 11 11 TRP A 158 LYS A 162 5 5
SHEET 1 A 3 ARG A 14 LYS A 19 0 SHEET 2 A 3 TYR A 25 GLY A 28 -1 O THR A 26 N TYR A 18 SHEET 3 A 3 HIS A 31 THR A 34 -1 N HIS A 31 O ILE A 27
LINK S2 BME A 901 S2 BME A 901 1555 5555 2.09 LINK S2 BME A 902 S2 BME A 903 1555 1555 2.00
SITE 1 AC1 5 LYS A 124 THR A 142 ASN A 144 ARG A 145 SITE 2 AC1 5 HOH A 209 SITE 1 AC2 1 HOH A 215 SITE 1 AC3 2 ALA A 99 XE A 502 SITE 1 AC4 2 LEU A 118 XE A 502 SITE 1 AC5 4 VAL A 111 LEU A 118 XE A 500 XE A 501 SITE 1 AC6 4 ASP A 72 VAL A 75 LEU A 79 TYR A 88 SITE 1 AC7 1 BME A 903 SITE 1 AC8 3 ALA A 93 ILE A 100 BME A 902
CRYST1 60.947 60.947 97.583 90.00 90.00 120.00 P 32 2 1 6
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 0.016408 0.009473 0.000000 0.00000
SCALE2 0.000000 0.018946 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010248 0.00000