HEADER HYDROLASE 24-APR-12 4ET9 TITLE HEN EGG-WHITE LYSOZYME SOLVED FROM 5 FS FREE-ELECTRON LASER PULSE DATA 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 6 16-AUG-23 4ET9 1 REMARK REVDAT 5 14-FEB-18 4ET9 1 REMARK REVDAT 4 15-NOV-17 4ET9 1 REMARK REVDAT 3 18-NOV-15 4ET9 1 REMARK REVDAT 2 08-AUG-12 4ET9 1 JRNL REVDAT 1 13-JUN-12 4ET9 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.480 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 9743 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 497 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 35.3360 - 3.0156 0.99 2464 126 0.1924 0.2296 REMARK 3 2 3.0156 - 2.3937 0.99 2317 128 0.1765 0.2080 REMARK 3 3 2.3937 - 2.0912 0.98 2266 120 0.1735 0.2249 REMARK 3 4 2.0912 - 1.9000 0.97 2199 123 0.2301 0.2690 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 : 0.29 REMARK 3 B_SOL : 46.79 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.950 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) : -1.31090 REMARK 3 B22 (A**2) : -1.31090 REMARK 3 B33 (A**2) : 2.62190 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 : 1.025 1381 REMARK 3 CHIRALITY : 0.076 144 REMARK 3 PLANARITY : 0.003 181 REMARK 3 DIHEDRAL : 14.114 365 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 4ET9 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_1000072040. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 10575 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : CXI REMARK 200 X-RAY GENERATOR MODEL : SLAC LCLS BEAMLINE CXI REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.32 REMARK 200 MONOCHROMATOR : CXI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9743 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 35.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 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 (%) : 91.2 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 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 (%): 40.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AFTER CRYSTALLIZATION, THE SOLUTION REMARK 280 USED FOR GROWING THE CRYSTALS (20 % NACL, 6 % PEG 6000, 1 M NA REMARK 280 ACETATE PH 3.0) WAS EXCHANGED FOR STORAGE SOLUTION (10 % NACL, REMARK 280 1.0 M NA ACETATE PH 3.4), BATCH, 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 19.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.50000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.50000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.50000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.50000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.50000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.50000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.50000 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 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 NA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ET8 RELATED DB: PDB REMARK 900 RELATED ID: 4ETA 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 4ET9 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 NA A 201 1 HET CL A 202 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 2 NA NA 1+ FORMUL 3 CL CL 1- FORMUL 4 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 2.02 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.02 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.01 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.03 SITE 1 AC1 3 ASN A 65 SER A 72 ARG A 73 SITE 1 AC2 2 TYR A 23 ASN A 113 CRYST1 79.000 79.000 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 0.012658 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012658 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026316 0.00000