HEADER HYDROLASE 11-JAN-21 7BHN TITLE CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME USING DROP-ON-DROP SFX TITLE 2 METHOD - 2 S MIXING WITH N-ACETYL-D-GLUCOSAMINE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 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, SFX, XFEL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.BUTRYN,A.M.ORVILLE REVDAT 4 16-OCT-24 7BHN 1 REMARK REVDAT 3 31-JAN-24 7BHN 1 REMARK REVDAT 2 04-AUG-21 7BHN 1 JRNL REVDAT 1 21-JUL-21 7BHN 0 JRNL AUTH A.BUTRYN,P.S.SIMON,P.ALLER,P.HINCHLIFFE,R.N.MASSAD,G.LEEN, JRNL AUTH 2 C.L.TOOKE,I.BOGACZ,I.S.KIM,A.BHOWMICK,A.S.BREWSTER, JRNL AUTH 3 N.E.DEVENISH,J.BREM,J.J.A.G.KAMPS,P.A.LANG,P.RABE,D.AXFORD, JRNL AUTH 4 J.H.BEALE,B.DAVY,A.EBRAHIM,J.ORLANS,S.L.S.STORM,T.ZHOU, JRNL AUTH 5 S.OWADA,R.TANAKA,K.TONO,G.EVANS,R.L.OWEN,F.A.HOULE, JRNL AUTH 6 N.K.SAUTER,C.J.SCHOFIELD,J.SPENCER,V.K.YACHANDRA,J.YANO, JRNL AUTH 7 J.F.KERN,A.M.ORVILLE JRNL TITL AN ON-DEMAND, DROP-ON-DROP METHOD FOR STUDYING ENZYME JRNL TITL 2 CATALYSIS BY SERIAL CRYSTALLOGRAPHY. JRNL REF NAT COMMUN V. 12 4461 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34294694 JRNL DOI 10.1038/S41467-021-24757-7 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.1_3865 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 21738 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1079 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 34.2300 - 2.9000 1.00 2752 151 0.1607 0.1647 REMARK 3 2 2.9000 - 2.3000 1.00 2611 152 0.1764 0.1949 REMARK 3 3 2.3000 - 2.0100 1.00 2590 134 0.1646 0.1790 REMARK 3 4 2.0100 - 1.8300 1.00 2557 128 0.1704 0.2067 REMARK 3 5 1.8300 - 1.7000 1.00 2577 130 0.1999 0.2390 REMARK 3 6 1.7000 - 1.6000 1.00 2532 129 0.2455 0.3085 REMARK 3 7 1.6000 - 1.5200 1.00 2541 119 0.3465 0.3566 REMARK 3 8 1.5200 - 1.4500 0.99 2499 136 0.4207 0.3899 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) : 0.227 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.442 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.13 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 : 0.005 1091 REMARK 3 ANGLE : 0.765 1489 REMARK 3 CHIRALITY : 0.079 158 REMARK 3 PLANARITY : 0.004 198 REMARK 3 DIHEDRAL : 11.772 397 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 7BHN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1292113414. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 308 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : BL2 REMARK 200 X-RAY GENERATOR MODEL : SACLA BEAMLINE BL2 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.24 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21782 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 55.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 125.3 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 68.7730 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 : 0.648 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: 4ETA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M CITRIC ACID, 20% (W/V) NACL, 5% REMARK 280 (W/V) PEG 6000, PH 3.0, BATCH MODE, TEMPERATURE 295K 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 19.00100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.40200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.40200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.50150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.40200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.40200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.50050 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.40200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.40200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.50150 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.40200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.40200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.50050 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 19.00100 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: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 336 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 351 LIES ON A SPECIAL POSITION. 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 LYS A 97 CG CD CE NZ REMARK 470 ARG A 125 CG CD 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 ARG A 68 26.70 -140.90 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 206 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 60 O REMARK 620 2 CYS A 64 O 87.3 REMARK 620 3 SER A 72 OG 88.7 164.7 REMARK 620 4 ARG A 73 O 92.0 92.3 102.6 REMARK 620 5 HOH A 331 O 99.4 85.7 80.4 168.3 REMARK 620 6 HOH A 358 O 173.9 98.4 85.3 89.9 79.1 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7BHK RELATED DB: PDB REMARK 900 RESTING STATE REMARK 900 RELATED ID: 7BHL RELATED DB: PDB REMARK 900 0.2 S AFTER MIXING WITH N-ACETYL-D-GLUCOSAMINE REMARK 900 RELATED ID: 7BHM RELATED DB: PDB REMARK 900 0.7 S AFTER MIXING WITH N-ACETYL-D-GLUCOSAMINE DBREF 7BHN 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 NDG A 201 15 HET CL A 202 1 HET CL A 203 1 HET CL A 204 1 HET CL A 205 1 HET NA A 206 1 HETNAM NDG 2-ACETAMIDO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETSYN NDG N-ACETYL-ALPHA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 NDG ALPHA-D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2- HETSYN 3 NDG ACETAMIDO-2-DEOXY-GLUCOSE; 2-(ACETYLAMINO)-2-DEOXY-A- HETSYN 4 NDG D-GLUCOPYRANOSE FORMUL 2 NDG C8 H15 N O6 FORMUL 3 CL 4(CL 1-) FORMUL 7 NA NA 1+ FORMUL 8 HOH *78(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 2.01 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.03 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.04 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.03 LINK O SER A 60 NA NA A 206 1555 1555 2.37 LINK O CYS A 64 NA NA A 206 1555 1555 2.40 LINK OG SER A 72 NA NA A 206 1555 1555 2.51 LINK O ARG A 73 NA NA A 206 1555 1555 2.54 LINK NA NA A 206 O HOH A 331 1555 1555 2.48 LINK NA NA A 206 O HOH A 358 1555 1555 2.41 CRYST1 78.804 78.804 38.002 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 0.012690 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012690 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026314 0.00000