HEADER HYDROLASE 08-SEP-15 5DM9
TITLE XFEL STRUCTURE OF HEN EGG-WHITE LYSOZYME SOLVED USING A DROPLET
TITLE 2 INJECTOR AT SACLA
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: CHICKEN;
SOURCE 4 ORGANISM_TAXID: 9031
KEYWDS LYSOZYME, SERIAL FEMTOSECOND CRYSTALLOGRAPHY, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.KOBAYASHI,E.NANGO
REVDAT 5 08-NOV-23 5DM9 1 REMARK
REVDAT 4 06-SEP-23 5DM9 1 REMARK
REVDAT 3 14-MAR-18 5DM9 1 JRNL
REVDAT 2 24-JAN-18 5DM9 1 REMARK
REVDAT 1 13-APR-16 5DM9 0
JRNL AUTH F.MAFUNE,K.MIYAJIMA,K.TONO,Y.TAKEDA,J.Y.KOHNO,N.MIYAUCHI,
JRNL AUTH 2 J.KOBAYASHI,Y.JOTI,E.NANGO,S.IWATA,M.YABASHI
JRNL TITL MICROCRYSTAL DELIVERY BY PULSED LIQUID DROPLET FOR SERIAL
JRNL TITL 2 FEMTOSECOND CRYSTALLOGRAPHY.
JRNL REF ACTA CRYSTALLOGR D STRUCT V. 72 520 2016
JRNL REF 2 BIOL
JRNL REFN ISSN 2059-7983
JRNL PMID 27050131
JRNL DOI 10.1107/S2059798316001480
REMARK 2
REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.9_1692
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) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.60
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.800
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 5743
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.184
REMARK 3 R VALUE (WORKING SET) : 0.182
REMARK 3 FREE R VALUE : 0.212
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.540
REMARK 3 FREE R VALUE TEST SET COUNT : 261
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 39.6058 - 2.8981 1.00 2806 139 0.1716 0.1998
REMARK 3 2 2.8981 - 2.3004 1.00 2676 122 0.2092 0.2431
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.540
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) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
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 : 0.002 1025
REMARK 3 ANGLE : 0.626 1381
REMARK 3 CHIRALITY : 0.024 144
REMARK 3 PLANARITY : 0.002 181
REMARK 3 DIHEDRAL : 11.230 365
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 5DM9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-SEP-15.
REMARK 100 THE DEPOSITION ID IS D_1000213399.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 18-MAY-15
REMARK 200 TEMPERATURE (KELVIN) : 293
REMARK 200 PH : 3.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER
REMARK 200 BEAMLINE : BL3
REMARK 200 X-RAY GENERATOR MODEL : SACLA BEAMLINE BL3
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.77
REMARK 200 MONOCHROMATOR : SI 111
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MPCCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5774
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
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 (%) : 100.0
REMARK 200 DATA REDUNDANCY : 85.00
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.6600
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 53.10
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: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: REFMAC 5.8.0049
REMARK 200 STARTING MODEL: 1VDS
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 40.79
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, SODIUM CHLORIDE, SODIUM
REMARK 280 ACETATE, PH 3.0, BATCH MODE, TEMPERATURE 290K
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 19.00000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.60000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.60000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.50000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.60000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.60000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.50000
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.60000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.60000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.50000
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.60000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.60000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.50000
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 19.00000
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 TOTAL BURIED SURFACE AREA: 400 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 6540 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL
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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 346 LIES ON A SPECIAL POSITION.
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 203 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER A 60 O
REMARK 620 2 CYS A 64 O 78.7
REMARK 620 3 SER A 72 OG 86.6 152.5
REMARK 620 4 ARG A 73 O 96.0 91.3 113.4
REMARK 620 5 HOH A 323 O 91.5 82.3 74.9 169.0
REMARK 620 6 HOH A 340 O 171.4 99.1 91.9 92.4 79.9
REMARK 620 N 1 2 3 4 5
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 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 203
DBREF 5DM9 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
HET CL A 202 1
HET NA A 203 1
HETNAM CL CHLORIDE ION
HETNAM NA SODIUM ION
FORMUL 2 CL 2(CL 1-)
FORMUL 4 NA NA 1+
FORMUL 5 HOH *64(H2 O)
HELIX 1 AA1 GLY A 4 HIS A 15 1 12
HELIX 2 AA2 ASN A 19 TYR A 23 5 5
HELIX 3 AA3 SER A 24 ASN A 37 1 14
HELIX 4 AA4 PRO A 79 SER A 85 5 7
HELIX 5 AA5 ILE A 88 SER A 100 1 13
HELIX 6 AA6 ASN A 103 ALA A 107 5 5
HELIX 7 AA7 TRP A 108 CYS A 115 1 8
HELIX 8 AA8 ASP A 119 ILE A 124 5 6
SHEET 1 AA1 3 THR A 43 ARG A 45 0
SHEET 2 AA1 3 THR A 51 TYR A 53 -1 O ASP A 52 N ASN A 44
SHEET 3 AA1 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 2.03
SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.03
SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.03
LINK O SER A 60 NA NA A 203 1555 1555 2.42
LINK O CYS A 64 NA NA A 203 1555 1555 2.48
LINK OG SER A 72 NA NA A 203 1555 1555 2.52
LINK O ARG A 73 NA NA A 203 1555 1555 2.63
LINK NA NA A 203 O HOH A 323 1555 1555 2.53
LINK NA NA A 203 O HOH A 340 1555 1555 2.50
SITE 1 AC1 2 TYR A 23 ASN A 113
SITE 1 AC2 6 SER A 60 CYS A 64 SER A 72 ARG A 73
SITE 2 AC2 6 HOH A 323 HOH A 340
CRYST1 79.200 79.200 38.000 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 0.012626 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012626 0.000000 0.00000
SCALE3 0.000000 0.000000 0.026316 0.00000
(ATOM LINES ARE NOT SHOWN.)
END