HEADER HYDROLASE 05-DEC-12 3ZEK TITLE HEN EGG-WHITE LYSOZYME STRUCTURE DETERMINED AT ROOM TEMPERATURE BY IN- TITLE 2 SITU DIFFRACTION IN CHIPX 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, GAL D 4; 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 MICROFLUIDIC CHIP, IN-SITU DIFFRACTION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.PINKER,B.LORBER,C.SAUTER REVDAT 3 20-DEC-23 3ZEK 1 REMARK REVDAT 2 06-MAR-19 3ZEK 1 REMARK REVDAT 1 26-DEC-12 3ZEK 0 JRNL AUTH F.PINKER,M.BRUN,P.MORIN,A.DEMAN,J.CHATEAUX,V.OLIERIC, JRNL AUTH 2 C.STIRNIMANN,B.LORBER,N.TERRIER,R.FERRIGNO,C.SAUTER JRNL TITL CHIPX: A NOVEL MICROFLUIDIC CHIP FOR COUNTER- DIFFUSION JRNL TITL 2 CRYSTALLIZATION OF BIOMOLECULES AND IN SITU CRYSTAL ANALYSIS JRNL TITL 3 AT ROOM TEMPERATURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.DHOUIB,C.KHAN MALEK,W.PFLEGING,B.GAUTHIER-MANUEL, REMARK 1 AUTH 2 R.DUFFAIT,G.THUILLIER,R.FERRIGNO,L.JACQUAMET,J.OHANA, REMARK 1 AUTH 3 J.FERRER,A.THEOBALD-DIETRICH,R.GIEGE,B.LORBER,C.SAUTER REMARK 1 TITL MICROFLUIDIC CHIPS FOR THE CRYSTALLIZATION OF REMARK 1 TITL 2 BIOMACROMOLECULES BY COUNTER-DIFFUSION AND ON-CHIP CRYSTAL REMARK 1 TITL 3 X-RAY ANALYSIS. REMARK 1 REF LAB CHIP V. 9 1412 2009 REMARK 1 REFN ISSN 1473-0197 REMARK 1 PMID 19417908 REMARK 1 DOI 10.1039/B819362B REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 3.280 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 22684 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1134 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 27.4203 - 2.8589 0.99 2868 151 0.1529 0.1544 REMARK 3 2 2.8589 - 2.2695 0.99 2732 144 0.1768 0.1991 REMARK 3 3 2.2695 - 1.9827 1.00 2709 143 0.1656 0.2043 REMARK 3 4 1.9827 - 1.8015 1.00 2688 141 0.1738 0.1737 REMARK 3 5 1.8015 - 1.6724 0.99 2682 142 0.1842 0.2305 REMARK 3 6 1.6724 - 1.5738 0.99 2646 138 0.1835 0.2062 REMARK 3 7 1.5738 - 1.4950 0.99 2641 138 0.2081 0.2001 REMARK 3 8 1.4950 - 1.4299 0.97 2584 137 0.2174 0.2431 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) : 18.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.00 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 1025 REMARK 3 ANGLE : 0.937 1381 REMARK 3 CHIRALITY : 0.074 144 REMARK 3 PLANARITY : 0.003 181 REMARK 3 DIHEDRAL : 12.364 365 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 3ZEK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1290054994. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA 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 PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22727 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 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: PDB ENTRY 1IEE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LYSOZYME WAS CRYSTALLIZED AT 293 K BY REMARK 280 COUNTER-DIFFUSION IN A CHIPX MICROFLUIDIC DEVICE. MICROFLUIDIC REMARK 280 CHANNELS WERE FILLED WITH A 50 MG/ML LYSOZYME SOLUTION REMARK 280 CONTAINING 0.3% BETA-OCTYL-GLUCOSIDE (M/V) TO FACILITATE SAMPLE REMARK 280 LOADING BY CAPILLARITY. CRYSTALLANT RESERVOIRS WERE FILLED WITH REMARK 280 1 M NACL CONTAINING 30% (M/V) PEG-3350 OR 2 M NACL, AND 0.1 M REMARK 280 SODIUM ACETATE PH 4.5. 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 18.98500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.62500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.62500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.47750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.62500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.62500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.49250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.62500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.62500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.47750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.62500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.62500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.49250 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 18.98500 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 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 A2018 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2037 LIES ON A SPECIAL POSITION. 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 1130 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1131 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZEJ RELATED DB: PDB REMARK 900 THAUMATIN STRUCTURE DETERMINED AT ROOM TEMPERATURE BY IN -SITU REMARK 900 DIFFRACTION IN CHIPX DBREF 3ZEK 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 CL A1130 1 HET CL A1131 1 HETNAM CL CHLORIDE ION FORMUL 2 CL 2(CL 1-) FORMUL 4 HOH *82(H2 O) HELIX 1 1 GLY A 4 HIS A 15 1 12 HELIX 2 2 SER A 24 ASN A 37 1 14 HELIX 3 3 CYS A 80 SER A 85 5 6 HELIX 4 4 ILE A 88 SER A 100 1 13 HELIX 5 5 ASN A 103 ALA A 107 5 5 HELIX 6 6 TRP A 108 CYS A 115 1 8 HELIX 7 7 ASP A 119 ARG A 125 5 7 SHEET 1 AA 3 THR A 43 ARG A 45 0 SHEET 2 AA 3 THR A 51 TYR A 53 -1 O ASP A 52 N ASN A 44 SHEET 3 AA 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 2.03 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.03 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.03 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.03 SITE 1 AC1 2 TYR A 23 ASN A 113 SITE 1 AC2 2 SER A 24 GLY A 26 CRYST1 79.250 79.250 37.970 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 0.012618 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026337 0.00000