HEADER HYDROLASE 24-APR-12 4ETA
TITLE LYSOZYME, ROOM TEMPERATURE, 400 KGY DOSE
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 IV;
COMPND 5 EC: 3.2.1.17
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS;
SOURCE 3 ORGANISM_COMMON: BANTAM,CHICKENS;
SOURCE 4 ORGANISM_TAXID: 9031
KEYWDS LYSOZYME, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.BOUTET,L.LOMB,G.WILLIAMS,T.BARENDS,A.AQUILA,R.B.DOAK,U.WEIERSTALL,
AUTHOR 2 D.DEPONTE,J.STEINBRENER,R.SHOEMAN,M.MESSERSCHMIDT,A.BARTY,T.WHITE,
AUTHOR 3 S.KASSEMEYER,R.KIRIAN,M.SEIBERT,P.MONTANEZ,C.KENNEY,R.HERBST,P.HART,
AUTHOR 4 J.PINES,G.HALLER,S.GRUNER,H.PHILLLIP,M.TATE,M.HROMALIK,L.KOERNER,
AUTHOR 5 N.VAN BAKEL,J.MORSE,W.GHONSALVES,D.ARNLUND,M.BOGAN,C.CALEMANN,
AUTHOR 6 R.FROMME,C.HAMPTON,M.HUNTER,L.JOHANSSON,G.KATONA,C.KUPITZ,M.LIANG,
AUTHOR 7 A.MARTIN,K.NASS,L.REDECKE,F.STELLATO,N.TIMNEANU,D.WANG,N.ZATSEPIN,
AUTHOR 8 D.SCHAFER,K.DEFEVER,R.NEUTZE,P.FROMME,J.SPENCE,H.CHAPMAN,
AUTHOR 9 I.SCHLICHTING
REVDAT 3 15-NOV-17 4ETA 1 REMARK
REVDAT 2 08-AUG-12 4ETA 1 JRNL
REVDAT 1 13-JUN-12 4ETA 0
JRNL AUTH S.BOUTET,L.LOMB,G.J.WILLIAMS,T.R.BARENDS,A.AQUILA,R.B.DOAK,
JRNL AUTH 2 U.WEIERSTALL,D.P.DEPONTE,J.STEINBRENER,R.L.SHOEMAN,
JRNL AUTH 3 M.MESSERSCHMIDT,A.BARTY,T.A.WHITE,S.KASSEMEYER,R.A.KIRIAN,
JRNL AUTH 4 M.M.SEIBERT,P.A.MONTANEZ,C.KENNEY,R.HERBST,P.HART,J.PINES,
JRNL AUTH 5 G.HALLER,S.M.GRUNER,H.T.PHILIPP,M.W.TATE,M.HROMALIK,
JRNL AUTH 6 L.J.KOERNER,N.VAN BAKEL,J.MORSE,W.GHONSALVES,D.ARNLUND,
JRNL AUTH 7 M.J.BOGAN,C.CALEMAN,R.FROMME,C.Y.HAMPTON,M.S.HUNTER,
JRNL AUTH 8 L.C.JOHANSSON,G.KATONA,C.KUPITZ,M.LIANG,A.V.MARTIN,K.NASS,
JRNL AUTH 9 L.REDECKE,F.STELLATO,N.TIMNEANU,D.WANG,N.A.ZATSEPIN,
JRNL AUTH10 D.SCHAFER,J.DEFEVER,R.NEUTZE,P.FROMME,J.C.SPENCE,
JRNL AUTH11 H.N.CHAPMAN,I.SCHLICHTING
JRNL TITL HIGH-RESOLUTION PROTEIN STRUCTURE DETERMINATION BY SERIAL
JRNL TITL 2 FEMTOSECOND CRYSTALLOGRAPHY.
JRNL REF SCIENCE V. 337 362 2012
JRNL REFN ISSN 0036-8075
JRNL PMID 22653729
JRNL DOI 10.1126/SCIENCE.1217737
REMARK 2
REMARK 2 RESOLUTION. 1.91 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.91
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.46
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.050
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 3 NUMBER OF REFLECTIONS : 9851
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.161
REMARK 3 R VALUE (WORKING SET) : 0.160
REMARK 3 FREE R VALUE : 0.180
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090
REMARK 3 FREE R VALUE TEST SET COUNT : 501
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 35.4701 - 3.0315 0.99 2449 124 0.1660 0.1758
REMARK 3 2 3.0315 - 2.4063 1.00 2337 128 0.1717 0.1909
REMARK 3 3 2.4063 - 2.1022 1.00 2313 120 0.1426 0.1843
REMARK 3 4 2.1022 - 1.9100 1.00 2251 129 0.1384 0.1669
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.10
REMARK 3 SHRINKAGE RADIUS : 0.86
REMARK 3 K_SOL : 0.33
REMARK 3 B_SOL : 33.21
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.720
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.86700
REMARK 3 B22 (A**2) : -0.86700
REMARK 3 B33 (A**2) : 1.73390
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.006 1025
REMARK 3 ANGLE : 1.010 1381
REMARK 3 CHIRALITY : 0.078 144
REMARK 3 PLANARITY : 0.003 181
REMARK 3 DIHEDRAL : 13.815 365
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4ETA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-12.
REMARK 100 THE DEPOSITION ID IS D_1000072041.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 26-AUG-11
REMARK 200 TEMPERATURE (KELVIN) : 293
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X10SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97860
REMARK 200 MONOCHROMATOR : SI111
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10022
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 39.600
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6
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) : 1.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7
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: PHENIX
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.30
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: GROWN IN LINBRO PLATES IN HANGING OR
REMARK 280 SITTING DROP GEOMETRY. DROPS OF EQUAL VOLUME OF PROTEIN (20 MG/
REMARK 280 ML) AND RESERVOIR SOLUTION (1 M NAAC PH 3.0, 9-10 % NACL, 6 %
REMARK 280 PEG 6000) WERE MIXED. FOR THE MEASUREMENTS, THE CRYSTALS WERE
REMARK 280 EQUILIBRATED IN 1 M NAAC PH 3.4, 10 % NACL, VAPOR DIFFUSION,
REMARK 280 TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+1/2
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 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.10000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.65000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.65000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.65000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.65000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.65000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.55000
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.65000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.65000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.65000
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.65000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.65000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.55000
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 19.10000
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 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 201
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4ET8 RELATED DB: PDB
REMARK 900 RELATED ID: 4ET9 RELATED DB: PDB
REMARK 900 RELATED ID: 4ETB RELATED DB: PDB
REMARK 900 RELATED ID: 4ETC RELATED DB: PDB
REMARK 900 RELATED ID: 4ETD RELATED DB: PDB
REMARK 900 RELATED ID: 4ETE RELATED DB: PDB
DBREF 4ETA 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 CL A 201 1
HETNAM CL CHLORIDE ION
FORMUL 2 CL CL 1-
FORMUL 3 HOH *87(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 SER A 100 1 13
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 ILE A 124 5 6
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 2.03
SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.03
SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.04
SITE 1 AC1 2 TYR A 23 ASN A 113
CRYST1 79.300 79.300 38.200 90.00 90.00 90.00 P 43 21 2 8
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 0.012610 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012610 0.000000 0.00000
SCALE3 0.000000 0.000000 0.026178 0.00000
(ATOM LINES ARE NOT SHOWN.)
END