HEADER HYDROLASE 05-NOV-20 7AVG TITLE PERDEUTERATED HEN EGG-WHITE LYSOZYME AT 100 K COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.17; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_TAXID: 9031; SOURCE 4 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS PERDEUTERATED, LYSOZYME, HEWL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.RAMOS,V.LAUX,M.HAERTLEIN,E.ERBA BOERI,V.T.FORSYTH,E.MOSSOU, AUTHOR 2 S.LARSEN,A.E.LANGKILDE REVDAT 5 13-NOV-24 7AVG 1 REMARK REVDAT 4 31-JAN-24 7AVG 1 REMARK REVDAT 3 14-JUL-21 7AVG 1 SOURCE REVDAT 2 19-MAY-21 7AVG 1 JRNL REVDAT 1 12-MAY-21 7AVG 0 JRNL AUTH J.RAMOS,V.LAUX,M.HAERTLEIN,E.BOERI ERBA,K.E.MCAULEY, JRNL AUTH 2 V.T.FORSYTH,E.MOSSOU,S.LARSEN,A.E.LANGKILDE JRNL TITL STRUCTURAL INSIGHTS INTO PROTEIN FOLDING, STABILITY AND JRNL TITL 2 ACTIVITY USING IN VIVO PERDEUTERATION OF HEN EGG-WHITE JRNL TITL 3 LYSOZYME. JRNL REF IUCRJ V. 8 372 2021 JRNL REFN ESSN 2052-2525 JRNL PMID 33953924 JRNL DOI 10.1107/S2052252521001299 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 49982 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.121 REMARK 3 R VALUE (WORKING SET) : 0.121 REMARK 3 FREE R VALUE : 0.134 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2400 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 32.0100 - 2.5700 0.99 2834 147 0.1546 0.1557 REMARK 3 2 2.5700 - 2.0400 0.99 2838 149 0.1285 0.1377 REMARK 3 3 2.0400 - 1.7800 0.99 2843 148 0.1216 0.1214 REMARK 3 4 1.7800 - 1.6200 0.99 2834 149 0.1148 0.1328 REMARK 3 5 1.6200 - 1.5000 0.99 2844 146 0.1012 0.1276 REMARK 3 6 1.5000 - 1.4200 0.99 2820 138 0.1012 0.1260 REMARK 3 7 1.4200 - 1.3400 0.98 2788 147 0.0947 0.1155 REMARK 3 8 1.3400 - 1.2900 0.98 2823 145 0.0940 0.1095 REMARK 3 9 1.2900 - 1.2400 0.98 2808 143 0.0867 0.1121 REMARK 3 10 1.2400 - 1.1900 0.98 2805 147 0.0908 0.1129 REMARK 3 11 1.1900 - 1.1600 0.97 2786 144 0.0909 0.1013 REMARK 3 12 1.1600 - 1.1200 0.97 2786 137 0.0946 0.1205 REMARK 3 13 1.1200 - 1.0900 0.97 2767 135 0.0966 0.1329 REMARK 3 14 1.0900 - 1.0700 0.96 2739 136 0.0999 0.1319 REMARK 3 15 1.0700 - 1.0400 0.96 2781 134 0.1053 0.1419 REMARK 3 16 1.0400 - 1.0200 0.96 2739 132 0.1137 0.1291 REMARK 3 17 1.0200 - 1.0000 0.95 2747 123 0.1218 0.1378 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) : 0.064 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.496 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.84 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 : 0.013 1376 REMARK 3 ANGLE : 1.616 1889 REMARK 3 CHIRALITY : 0.104 186 REMARK 3 PLANARITY : 0.015 271 REMARK 3 DIHEDRAL : 13.458 806 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 7AVG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1292111494. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX IV REMARK 200 BEAMLINE : BIOMAX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49991 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 32.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.08030 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.920 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4YEO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM NITRATE, SODIUM ACETATE PD 4.5, REMARK 280 PH 4.5, BATCH MODE, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 1440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 10.0 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 7 CD GLU A 7 OE1 0.136 REMARK 500 GLU A 7 CD GLU A 7 OE2 0.084 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLU A 7 OE1 - CD - OE2 ANGL. DEV. = 10.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 19 0.25 89.68 REMARK 500 ASP A 101 22.95 -78.14 REMARK 500 ARG A 114 -34.49 -137.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 435 DISTANCE = 6.34 ANGSTROMS DBREF 7AVG 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 NO3 A 201 4 HET NO3 A 202 4 HET NO3 A 203 4 HET NO3 A 204 4 HET ACT A 205 7 HET NO3 A 206 4 HET NO3 A 207 4 HET NO3 A 208 4 HET NO3 A 209 4 HET ACT A 210 7 HETNAM NO3 NITRATE ION HETNAM ACT ACETATE ION FORMUL 2 NO3 8(N O3 1-) FORMUL 6 ACT 2(C2 H3 O2 1-) FORMUL 12 HOH *135(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 ASP A 101 1 14 HELIX 6 AA6 GLY A 104 ALA A 107 5 4 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 2.02 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.05 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.03 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.02 CRYST1 26.670 30.970 33.740 89.44 72.82 67.50 P 1 1 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 0.037495 -0.015529 -0.013503 0.00000 SCALE2 0.000000 0.034949 0.004116 0.00000 SCALE3 0.000000 0.000000 0.031237 0.00000