PDB Short entry for 1SFB HEADER HYDROLASE 19-FEB-04 1SFB TITLE BINDING OF PENTA-N-ACETYLCHITOPENTAOSE TO HEW LYSOZYME: A POWDER TITLE 2 DIFFRACTION STUDY COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C; ALLERGEN GAL D 4; 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 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS POWDER DIFFRACTION; RIETVELD REFINEMENT; LYSOZYME, HYDROLASE EXPDTA POWDER DIFFRACTION AUTHOR R.B.VON DREELE REVDAT 5 29-JUL-20 1SFB 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 13-JUL-11 1SFB 1 VERSN REVDAT 3 24-FEB-09 1SFB 1 VERSN REVDAT 2 28-DEC-04 1SFB 1 JRNL REVDAT 1 02-MAR-04 1SFB 0 JRNL AUTH R.B.VON DREELE JRNL TITL BINDING OF N-ACETYLGLUCOSAMINE OLIGOSACCHARIDES TO HEN JRNL TITL 2 EGG-WHITE LYSOZYME: A POWDER DIFFRACTION STUDY. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 61 22 2005 JRNL REFN ISSN 0907-4449 JRNL PMID 15608372 JRNL DOI 10.1107/S0907444904025715 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.B.VON DREELE REMARK 1 TITL COMBINED RIETVELD AND STEREOCHEMICAL RESTRAINT REFINEMENT OF REMARK 1 TITL 2 A PROTEIN CRYSTAL STRUCTURE REMARK 1 REF J.APPL.CRYSTALLOGR. V. 32 1084 1999 REMARK 1 REFN ISSN 0021-8898 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.B.VON DREELE,P.W.STEPHENS,R.H.BLESSING,G.D.SMITH REMARK 1 TITL THE FIRST PROTEIN CRYSTAL STRUCTURE DETERMINED FROM HIGH REMARK 1 TITL 2 RESOLUTION X-RAY POWDER DIFFRACTION DATA: A VARIANT OF THE REMARK 1 TITL 3 T3R3 HUMAN INSULIN ZINC COMPLEX PRODUCED BY GRINDING REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 56 1549 2000 REMARK 1 REFN ISSN 0907-4449 REMARK 1 REFERENCE 3 REMARK 1 AUTH R.B.VON DREELE REMARK 1 TITL BINDING OF N-ACETYLGLUCOASMINE TO CHICKEN EGG LYSOZYME: A REMARK 1 TITL 2 POWDER DIFFRACTION STUDY REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 57 1836 2001 REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 4 REMARK 4 1SFB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000021660. REMARK 250 REMARK 250 EXPERIMENTAL DETAILS REMARK 250 EXPERIMENT TYPE : POWDER DIFFRACTION REMARK 250 DATE OF DATA COLLECTION : 21-JUL-01 REMARK 250 REMARK 250 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 APPLY THE FOLLOWING TO CHAINS: A, 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 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 ASP A 119 CB ASP A 119 CG 0.161 REMARK 500 ASP A 119 CG ASP A 119 OD2 0.216 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 CYS A 64 CA - CB - SG ANGL. DEV. = 11.8 DEGREES REMARK 500 PRO A 70 C - N - CD ANGL. DEV. = -22.9 DEGREES REMARK 500 ASP A 119 CB - CG - OD1 ANGL. DEV. = -7.5 DEGREES REMARK 500 ASP A 119 CB - CG - OD2 ANGL. DEV. = 14.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 5 0.15 SIDE CHAIN REMARK 500 ARG A 14 0.13 SIDE CHAIN REMARK 500 ARG A 21 0.14 SIDE CHAIN REMARK 500 ARG A 45 0.25 SIDE CHAIN REMARK 500 ARG A 61 0.20 SIDE CHAIN REMARK 500 ARG A 68 0.08 SIDE CHAIN REMARK 500 ARG A 112 0.08 SIDE CHAIN REMARK 500 ARG A 125 0.22 SIDE CHAIN REMARK 500 ARG A 128 0.25 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JA7 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH N-ACETYLGLUCOSAMINE REMARK 900 RELATED ID: 1SF4 RELATED DB: PDB REMARK 900 RELATED ID: 1SF6 RELATED DB: PDB REMARK 900 RELATED ID: 1SF7 RELATED DB: PDB REMARK 900 RELATED ID: 1SFG RELATED DB: PDB DBREF 1SFB A 1 129 UNP P00698 LYC_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 NAG B 1 15 HET NAG B 2 14 HET NAG B 3 14 HET NAG B 4 14 HET NAG B 5 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE FORMUL 2 NAG 5(C8 H15 N O6) HELIX 1 1 ARG A 5 ARG A 14 5 10 HELIX 2 2 SER A 24 SER A 36 1 13 HELIX 3 3 CYS A 80 SER A 85 1 6 HELIX 4 4 SER A 91 ILE A 98 1 8 HELIX 5 5 ASN A 103 TRP A 108 5 6 HELIX 6 6 VAL A 109 ARG A 114 1 6 HELIX 7 7 ASP A 119 TRP A 123 5 5 SHEET 1 A 2 ASP A 52 TYR A 53 0 SHEET 2 A 2 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 2.05 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.03 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.48 LINK O4 NAG B 2 C1 NAG B 3 1555 1555 1.48 LINK O4 NAG B 3 C1 NAG B 4 1555 1555 1.48 LINK O4 NAG B 4 C1 NAG B 5 1555 1555 1.49 CRYST1 79.000 79.000 38.137 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 0.012658 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012658 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026221 0.00000