HEADER LYSOZYME 13-OCT-96 1JUG TITLE LYSOZYME FROM ECHIDNA MILK (TACHYGLOSSUS ACULEATUS) 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: TACHYGLOSSUS ACULEATUS; SOURCE 3 ORGANISM_COMMON: AUSTRALIAN ECHIDNA; SOURCE 4 ORGANISM_TAXID: 9261; SOURCE 5 VARIANT: VARIANT I; SOURCE 6 SECRETION: MILK KEYWDS LYSOZYME, CALCIUM-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.M.GUSS REVDAT 3 09-AUG-23 1JUG 1 REMARK LINK REVDAT 2 24-FEB-09 1JUG 1 VERSN REVDAT 1 21-APR-97 1JUG 0 JRNL AUTH J.M.GUSS,M.MESSER,M.COSTELLO,K.HARDY,V.KUMAR JRNL TITL STRUCTURE OF THE CALCIUM-BINDING ECHIDNA MILK LYSOZYME AT JRNL TITL 2 1.9 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 53 355 1997 JRNL REFN ISSN 0907-4449 JRNL PMID 15299900 JRNL DOI 10.1107/S0907444996015831 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 8038 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT (EXCEPT LAST ROUND REMARK 3 OF 4 CYCLES) REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.600 REMARK 3 FREE R VALUE TEST SET COUNT : 852 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1690 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1680 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.600 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 852 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 8038 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 979 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 65 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 7.00 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.014 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.042 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.041 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.137 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.190 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.250 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.200 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 3.600 ; 5.000 REMARK 3 STAGGERED (DEGREES) : 22.000; 20.000 REMARK 3 TRANSVERSE (DEGREES) : 23.000; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.400 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.100 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.100 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.700 ; 3.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JUG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174373. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : SEP-94 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8418 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : 0.07700 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.14200 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 4LYZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.3 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 20.99000 REMARK 290 SMTRY3 2 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 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 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 ARG A 41 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 SER A 72 N - CA - CB ANGL. DEV. = -9.1 DEGREES REMARK 500 ASP A 85 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 86 CB - CG - OD2 ANGL. DEV. = 9.2 DEGREES REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 10.4 DEGREES REMARK 500 ASP A 90 CB - CG - OD1 ANGL. DEV. = 9.4 DEGREES REMARK 500 ASP A 91 CB - CG - OD1 ANGL. DEV. = -9.3 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 LYS A 68 14.53 -142.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 HIS A 45 14.01 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 CA A 126 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 82 O REMARK 620 2 ASP A 85 OD1 83.1 REMARK 620 3 ASP A 87 O 165.2 83.9 REMARK 620 4 ASP A 90 OD1 93.8 140.1 91.8 REMARK 620 5 ASP A 91 OD1 100.7 142.5 93.8 77.2 REMARK 620 6 HOH A 128 O 92.5 72.6 90.2 147.3 70.1 REMARK 620 7 HOH A 130 O 84.3 74.4 85.6 65.7 142.9 146.9 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CA BINDING SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 126 DBREF 1JUG A 1 125 UNP P37156 LYSC1_TACAC 1 125 SEQRES 1 A 125 LYS ILE LEU LYS LYS GLN GLU LEU CYS LYS ASN LEU VAL SEQRES 2 A 125 ALA GLN GLY MET ASN GLY TYR GLN HIS ILE THR LEU PRO SEQRES 3 A 125 ASN TRP VAL CYS THR ALA PHE HIS GLU SER SER TYR ASN SEQRES 4 A 125 THR ARG ALA THR ASN HIS ASN THR ASP GLY SER THR ASP SEQRES 5 A 125 TYR GLY ILE LEU GLN ILE ASN SER ARG TYR TRP CYS HIS SEQRES 6 A 125 ASP GLY LYS THR PRO GLY SER LYS ASN ALA CYS ASN ILE SEQRES 7 A 125 SER CYS SER LYS LEU LEU ASP ASP ASP ILE THR ASP ASP SEQRES 8 A 125 LEU LYS CYS ALA LYS LYS ILE ALA GLY GLU ALA LYS GLY SEQRES 9 A 125 LEU THR PRO TRP VAL ALA TRP LYS SER LYS CYS ARG GLY SEQRES 10 A 125 HIS ASP LEU SER LYS PHE LYS CYS HET CA A 126 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *65(H2 O) HELIX 1 1 LYS A 5 ALA A 14 1 10 HELIX 2 2 TYR A 20 HIS A 22 5 3 HELIX 3 3 LEU A 25 SER A 36 1 12 HELIX 4 4 CYS A 80 LEU A 83 5 4 HELIX 5 5 THR A 89 ALA A 102 1 14 HELIX 6 6 VAL A 109 LYS A 114 1 6 HELIX 7 7 SER A 121 PHE A 123 5 3 SHEET 1 A 2 THR A 43 HIS A 45 0 SHEET 2 A 2 THR A 51 TYR A 53 -1 N ASP A 52 O ASN A 44 SSBOND 1 CYS A 9 CYS A 125 1555 1555 2.01 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.08 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.04 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.01 LINK O LYS A 82 CA CA A 126 1555 1555 2.32 LINK OD1 ASP A 85 CA CA A 126 1555 1555 2.29 LINK O ASP A 87 CA CA A 126 1555 1555 2.31 LINK OD1 ASP A 90 CA CA A 126 1555 1555 2.37 LINK OD1 ASP A 91 CA CA A 126 1555 1555 2.49 LINK CA CA A 126 O HOH A 128 1555 1555 2.32 LINK CA CA A 126 O HOH A 130 1555 1555 2.56 SITE 1 CAB 7 LYS A 82 ASP A 85 ASP A 87 ASP A 90 SITE 2 CAB 7 ASP A 91 HOH A 128 HOH A 130 SITE 1 AC1 7 LYS A 82 ASP A 85 ASP A 87 ASP A 90 SITE 2 AC1 7 ASP A 91 HOH A 128 HOH A 130 CRYST1 37.120 41.980 38.090 90.00 91.04 90.00 P 1 21 1 2 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 0.026940 0.000000 0.000489 0.00000 SCALE2 0.000000 0.023821 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026258 0.00000