HEADER HYDROLASE 05-NOV-20 7AVE TITLE PERDEUTERATED REFOLDED HEN EGG-WHITE LYSOZYME AT 100 K 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 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS PERDEUTERATED, REFOLDED, LYSOZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.RAMOS,V.LAUX,M.HAERTLEIN,E.ERBA BOERI,V.T.FORSYTH,S.LARSEN, AUTHOR 2 E.MOSSOU,A.E.LANGKILDE REVDAT 4 06-NOV-24 7AVE 1 REMARK REVDAT 3 31-JAN-24 7AVE 1 REMARK REVDAT 2 19-MAY-21 7AVE 1 JRNL REVDAT 1 12-MAY-21 7AVE 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. 0.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.15.2 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) : 0.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 52964 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.105 REMARK 3 R VALUE (WORKING SET) : 0.105 REMARK 3 FREE R VALUE : 0.115 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 2510 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 1.00 2867 150 0.1336 0.1451 REMARK 3 2 2.5700 - 2.0400 1.00 2857 150 0.1138 0.1205 REMARK 3 3 2.0400 - 1.7800 0.99 2858 149 0.1014 0.0935 REMARK 3 4 1.7800 - 1.6200 0.99 2850 147 0.0956 0.0979 REMARK 3 5 1.6200 - 1.5000 0.99 2859 146 0.0857 0.1026 REMARK 3 6 1.5000 - 1.4100 0.99 2837 136 0.0875 0.0993 REMARK 3 7 1.4100 - 1.3400 0.98 2786 149 0.0843 0.0997 REMARK 3 8 1.3400 - 1.2800 0.98 2850 142 0.0855 0.0962 REMARK 3 9 1.2800 - 1.2300 0.98 2810 142 0.0827 0.0891 REMARK 3 10 1.2300 - 1.1900 0.98 2794 140 0.0835 0.0980 REMARK 3 11 1.1900 - 1.1500 0.98 2804 141 0.0837 0.0980 REMARK 3 12 1.1500 - 1.1200 0.97 2811 135 0.0864 0.0958 REMARK 3 13 1.1200 - 1.0900 0.97 2787 137 0.0883 0.1145 REMARK 3 14 1.0900 - 1.0700 0.97 2775 134 0.0941 0.1132 REMARK 3 15 1.0700 - 1.0400 0.96 2777 126 0.1021 0.1124 REMARK 3 16 1.0400 - 1.0200 0.96 2776 138 0.1135 0.1236 REMARK 3 17 1.0200 - 1.0000 0.94 2719 111 0.1251 0.1372 REMARK 3 18 1.0000 - 0.9800 0.92 2636 137 0.1363 0.1407 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) : 0.050 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 9.365 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.96 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 : 0.008 1367 REMARK 3 ANGLE : 1.423 1874 REMARK 3 CHIRALITY : 0.096 183 REMARK 3 PLANARITY : 0.014 269 REMARK 3 DIHEDRAL : 13.458 805 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 7AVE 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_1292111401. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7293 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52966 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.980 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 (%) : 97.4 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.04240 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.0900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.27300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.210 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 (%): 27.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M SODIUM NITRATE, 0.05 M SODIUM REMARK 280 ACETATE PH 4.5, MICROBATCH, 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: 1450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6740 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 101 O HOH A 343 1554 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 0.091 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 7.58 85.94 REMARK 500 ASP A 101 21.61 -78.34 REMARK 500 ARG A 114 -32.18 -140.42 REMARK 500 REMARK 500 REMARK: NULL DBREF 7AVE A 0 129 UNP P00698 LYSC_CHICK 18 147 SEQRES 1 A 130 GLY LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET SEQRES 2 A 130 LYS ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU SEQRES 3 A 130 GLY ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE SEQRES 4 A 130 ASN THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR SEQRES 5 A 130 ASP TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS SEQRES 6 A 130 ASN ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN SEQRES 7 A 130 ILE PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SEQRES 8 A 130 SER VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN SEQRES 9 A 130 GLY MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS SEQRES 10 A 130 GLY 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 *136(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 2.04 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.05 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.04 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.03 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