HEADER HYDROLASE 05-OCT-18 6HU5 TITLE STRUCTURE OF HEWL BY ELECTRON DIFFRACTION AND MICROFOCUS DIFFRACTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME C; COMPND 3 CHAIN: A, B; 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, HEWL, ED, ELECTRON, DIFFRACTION, HYDROLASE, CRYSTAL, KEYWDS 2 CHLORIDE, HALOGEN, PROTEIN, DIMER, MICROFOCUS EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR G.GARAU REVDAT 3 17-JUL-19 6HU5 1 REMARK REVDAT 2 27-MAR-19 6HU5 1 JRNL REVDAT 1 23-JAN-19 6HU5 0 JRNL AUTH A.LANZA,E.MARGHERITIS,E.MUGNAIOLI,V.CAPPELLO,G.GARAU,M.GEMMI JRNL TITL NANOBEAM PRECESSION-ASSISTED 3D ELECTRON DIFFRACTION REVEALS JRNL TITL 2 A NEW POLYMORPH OF HEN EGG-WHITE LYSOZYME. JRNL REF IUCRJ V. 6 178 2019 JRNL REFN ESSN 2052-2525 JRNL PMID 30867915 JRNL DOI 10.1107/S2052252518017657 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 63.1 REMARK 3 NUMBER OF REFLECTIONS : 3840 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.300 REMARK 3 R VALUE (WORKING SET) : 0.298 REMARK 3 FREE R VALUE : 0.339 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.610 REMARK 3 FREE R VALUE TEST SET COUNT : 177 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 2.9700 - 2.8010 0.63 3663 177 0.2975 0.3390 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.860 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 : 0.004 2037 REMARK 3 ANGLE : 0.776 2761 REMARK 3 CHIRALITY : 0.047 286 REMARK 3 PLANARITY : 0.004 359 REMARK 3 DIHEDRAL : 13.180 1408 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 1:129) REMARK 3 ORIGIN FOR THE GROUP (A): -3.4312 -9.3926 26.2232 REMARK 3 T TENSOR REMARK 3 T11: 0.0061 T22: -0.2618 REMARK 3 T33: -0.0176 T12: 0.0250 REMARK 3 T13: 0.0314 T23: 0.0970 REMARK 3 L TENSOR REMARK 3 L11: 0.0278 L22: 0.1950 REMARK 3 L33: 0.1764 L12: -0.0099 REMARK 3 L13: 0.0017 L23: 0.0243 REMARK 3 S TENSOR REMARK 3 S11: 0.0165 S12: -0.0482 S13: -0.0125 REMARK 3 S21: 0.0139 S22: -0.0540 S23: 0.0583 REMARK 3 S31: 0.0932 S32: 0.0384 S33: -0.3486 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESSEQ 1:129) REMARK 3 ORIGIN FOR THE GROUP (A): 8.1831 -36.1018 12.3240 REMARK 3 T TENSOR REMARK 3 T11: 0.0216 T22: 0.1761 REMARK 3 T33: 0.2903 T12: 0.0256 REMARK 3 T13: -0.0572 T23: -0.1159 REMARK 3 L TENSOR REMARK 3 L11: 0.0711 L22: 0.0642 REMARK 3 L33: 0.0478 L12: -0.0021 REMARK 3 L13: -0.0313 L23: -0.0185 REMARK 3 S TENSOR REMARK 3 S11: -0.0301 S12: 0.0513 S13: -0.0465 REMARK 3 S21: -0.0787 S22: -0.0250 S23: -0.1316 REMARK 3 S31: -0.0610 S32: -0.0100 S33: -0.1019 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 6HU5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1200012310. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : 01-OCT-18 REMARK 240 TEMPERATURE (KELVIN) : 100.0 REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : ZEISS LIBRA120PLUS REMARK 240 DETECTOR TYPE : OTHER REMARK 240 ACCELERATION VOLTAGE (KV) : 120 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 3906 REMARK 240 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 240 RESOLUTION RANGE LOW (A) : 42.670 REMARK 240 DATA SCALING SOFTWARE : AIMLESS REMARK 240 COMPLETENESS FOR RANGE (%) : 66.5 REMARK 240 DATA REDUNDANCY : 2.800 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :2.80 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :2.97 REMARK 240 COMPLETENESS FOR SHELL (%) : 67.1 REMARK 240 DATA REDUNDANCY IN SHELL : 2.80 REMARK 240 R MERGE FOR SHELL (I) : 0.83900 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 240 SOFTWARE USED : XDS, CCP4 REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 27.19000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 LEU B 129 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG B 45 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 128 C O NE CZ NH1 NH2 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 ASN A 37 77.84 41.27 REMARK 500 PHE A 38 27.80 46.55 REMARK 500 THR A 47 -16.53 -41.95 REMARK 500 ASN A 77 83.66 52.54 REMARK 500 ALA A 122 -14.44 -39.53 REMARK 500 ASN B 37 77.85 41.37 REMARK 500 PHE B 38 27.84 46.44 REMARK 500 THR B 47 16.58 17.25 REMARK 500 ASP B 48 -1.73 -175.58 REMARK 500 ASN B 77 83.64 52.52 REMARK 500 ALA B 122 -14.47 -39.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN B 46 THR B 47 139.89 REMARK 500 REMARK 500 REMARK: NULL 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 CL B 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6HT2 RELATED DB: PDB REMARK 900 RELATED ID: 1LCN RELATED DB: PDB REMARK 900 RELATED ID: 1LKR RELATED DB: PDB REMARK 900 RELATED ID: 5OCV RELATED DB: PDB REMARK 900 RELATED ID: 5O4W RELATED DB: PDB REMARK 900 RELATED ID: 5A3E RELATED DB: PDB REMARK 900 RELATED ID: 5K7O RELATED DB: PDB REMARK 900 RELATED ID: 3J6K RELATED DB: PDB DBREF 6HU5 A 1 129 UNP P00698 LYSC_CHICK 19 147 DBREF 6HU5 B 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 SEQRES 1 B 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 B 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 B 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 B 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 B 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 B 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 B 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 B 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 B 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 B 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU HET CL A 201 1 HET CL B 201 1 HET CL B 202 1 HETNAM CL CHLORIDE ION FORMUL 3 CL 3(CL 1-) HELIX 1 AA1 GLY A 4 ARG A 14 1 11 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 LEU A 84 1 6 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 HELIX 9 AA9 GLY B 4 ARG B 14 1 11 HELIX 10 AB1 ASN B 19 TYR B 23 5 5 HELIX 11 AB2 SER B 24 ASN B 37 1 14 HELIX 12 AB3 PRO B 79 LEU B 84 1 6 HELIX 13 AB4 ILE B 88 SER B 100 1 13 HELIX 14 AB5 ASN B 103 ALA B 107 5 5 HELIX 15 AB6 TRP B 108 CYS B 115 1 8 HELIX 16 AB7 ASP B 119 ILE B 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 SHEET 1 AA2 3 THR B 43 ARG B 45 0 SHEET 2 AA2 3 THR B 51 TYR B 53 -1 O ASP B 52 N ASN B 44 SHEET 3 AA2 3 ILE B 58 ASN B 59 -1 O ILE B 58 N TYR B 53 SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.06 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.03 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.02 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.05 SSBOND 5 CYS B 6 CYS B 127 1555 1555 2.06 SSBOND 6 CYS B 30 CYS B 115 1555 1555 2.03 SSBOND 7 CYS B 64 CYS B 80 1555 1555 2.02 SSBOND 8 CYS B 76 CYS B 94 1555 1555 2.05 CISPEP 1 GLY A 71 SER A 72 0 -6.83 CISPEP 2 GLY B 71 SER B 72 0 -6.79 SITE 1 AC1 1 ARG A 114 SITE 1 AC2 1 ARG B 112 CRYST1 31.849 54.380 71.788 90.00 98.82 90.00 P 1 21 1 4 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 0.031398 0.000000 0.004871 0.00000 SCALE2 0.000000 0.018389 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014097 0.00000