HEADER BIOSYNTHETIC PROTEIN 01-AUG-22 7YNV TITLE CRYSTAL STRUCTURE OF PHOTOLYSED HEN EGG WHITE LYSOZYME INTRODUCED WITH TITLE 2 O-(2-NITROBENZYL)-L-TYROSINE 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; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: LYZ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NONNATURAL AMINO ACID CAGED AMINO ACID O-(2-NITROBENZYL)-L-TYROSINE KEYWDS 2 LYSOZYME CELL-FREE PROTEIN SYNTHESIS, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.HOSAKA,M.SHIROUZU REVDAT 3 29-NOV-23 7YNV 1 REMARK REVDAT 2 05-OCT-22 7YNV 1 JRNL REVDAT 1 21-SEP-22 7YNV 0 JRNL AUTH T.HOSAKA,K.KATSURA,Y.ISHIZUKA-KATSURA,K.HANADA,K.ITO, JRNL AUTH 2 Y.TOMABECHI,M.INOUE,R.AKASAKA,C.TAKEMOTO,M.SHIROUZU JRNL TITL CRYSTAL STRUCTURE OF AN ARCHAEAL TYROSYL-TRNA SYNTHETASE JRNL TITL 2 BOUND TO PHOTOCAGED L-TYROSINE AND ITS POTENTIAL APPLICATION JRNL TITL 3 TO TIME-RESOLVED X-RAY CRYSTALLOGRAPHY. JRNL REF INT J MOL SCI V. 23 2022 JRNL REFN ESSN 1422-0067 JRNL PMID 36142308 JRNL DOI 10.3390/IJMS231810399 REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 23825 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.390 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 39.1400 - 3.3500 1.00 1709 156 0.1649 0.1602 REMARK 3 2 3.3500 - 2.6600 1.00 1615 148 0.1699 0.1890 REMARK 3 3 2.6600 - 2.3200 1.00 1586 146 0.1704 0.1870 REMARK 3 4 2.3200 - 2.1100 1.00 1573 143 0.1637 0.1950 REMARK 3 5 2.1100 - 1.9600 1.00 1561 145 0.1689 0.2002 REMARK 3 6 1.9600 - 1.8400 1.00 1563 142 0.1770 0.2272 REMARK 3 7 1.8400 - 1.7500 1.00 1554 142 0.1846 0.2135 REMARK 3 8 1.7500 - 1.6800 1.00 1543 142 0.2114 0.2218 REMARK 3 9 1.6800 - 1.6100 1.00 1547 142 0.1821 0.1990 REMARK 3 10 1.6100 - 1.5600 1.00 1531 141 0.1872 0.2191 REMARK 3 11 1.5500 - 1.5100 1.00 1537 140 0.1841 0.2302 REMARK 3 12 1.5100 - 1.4600 1.00 1548 142 0.1916 0.2624 REMARK 3 13 1.4600 - 1.4200 1.00 1517 140 0.2161 0.2089 REMARK 3 14 1.4200 - 1.3900 0.93 1441 131 0.2306 0.2538 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.13 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7YNV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 3.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23873 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 39.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 22.06 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 17.84 REMARK 200 R MERGE FOR SHELL (I) : 0.37300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.010 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4YM8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% NACL, 8% PEG6000, 100 MM NA REMARK 280 -ACETATE (PH3.6), VAPOR DIFFUSION, SITTING DROP, 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 18.68500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.14000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.14000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.02750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.14000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.14000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.34250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.14000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.14000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.02750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.14000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.14000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.34250 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 18.68500 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: 290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 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 ARG A 68 29.73 -142.09 REMARK 500 REMARK 500 REMARK: NULL 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 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 60 O REMARK 620 2 CYS A 64 O 91.2 REMARK 620 3 SER A 72 OG 87.2 166.6 REMARK 620 4 ARG A 73 O 94.7 93.9 99.5 REMARK 620 5 HOH A 361 O 98.7 87.5 79.6 166.5 REMARK 620 6 HOH A 369 O 171.0 96.6 84.3 89.3 77.2 REMARK 620 N 1 2 3 4 5 DBREF 7YNV A 1 129 UNP P00698 LYSC_CHICK 19 147 SEQADV 7YNV VAL A 31 UNP P00698 ALA 49 VARIANT 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 VAL 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 HET CL A 203 1 HET CL A 204 1 HET CL A 205 1 HET CL A 206 1 HET ACT A 207 4 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM ACT ACETATE ION FORMUL 2 NA NA 1+ FORMUL 3 CL 5(CL 1-) FORMUL 8 ACT C2 H3 O2 1- FORMUL 9 HOH *138(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 ARG A 125 5 7 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 2.04 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.08 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.06 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.06 LINK O SER A 60 NA NA A 201 1555 1555 2.35 LINK O CYS A 64 NA NA A 201 1555 1555 2.36 LINK OG SER A 72 NA NA A 201 1555 1555 2.56 LINK O ARG A 73 NA NA A 201 1555 1555 2.41 LINK NA NA A 201 O HOH A 361 1555 1555 2.52 LINK NA NA A 201 O HOH A 369 1555 1555 2.46 CRYST1 78.280 78.280 37.370 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 0.012775 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026759 0.00000