HEADER HYDROLASE 19-DEC-11 2RSC TITLE SOLUTION STRUCTURE OF THE BOMBYX MORI LYSOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE; COMPND 5 EC: 3.2.1.17; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 3 ORGANISM_COMMON: SILK MOTH, SILKWORM; SOURCE 4 ORGANISM_TAXID: 7091; SOURCE 5 EXPRESSION_SYSTEM: CELL-FREE SYNTHESIS; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: P101129-01 KEYWDS LYSOZYME, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.SATO,N.TOCHIO,T.AIZAWA REVDAT 3 15-MAY-24 2RSC 1 REMARK REVDAT 2 14-JUN-23 2RSC 1 REMARK SEQADV REVDAT 1 26-DEC-12 2RSC 0 JRNL AUTH M.SATO,N.TOCHIO,S.WATANABE,T.KIGAWA,T.AIZAWA JRNL TITL SOLUTION STRUCTURE OF THE BOMBYX MORI LYSOZYME JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, CYANA, AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM (AMBER), GUNTERT, REMARK 3 MUMENTHALER AND WUTHRICH (CYANA), CASE, DARDEN, REMARK 3 CHEATHAM, III, SIMMERLING, WANG, DUKE, LUO, ... REMARK 3 AND KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RSC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000150225. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 3.8 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM SODIUM ACETATE-1, 100 MM REMARK 210 SODIUM CHLORIDE-2, 0.02 % SODIUM REMARK 210 AZIDE-3, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CYANA, NMRPIPE, REMARK 210 NMRVIEW, KUJIRA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, DGSA REMARK 210 -DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 2 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 11 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.0 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 1 TRP A 61 -51.11 -147.33 REMARK 500 1 PHE A 100 -15.84 -142.78 REMARK 500 1 HIS A 109 -32.14 -136.91 REMARK 500 2 TYR A 60 -59.10 -130.77 REMARK 500 2 PHE A 100 -10.32 -142.21 REMARK 500 2 HIS A 109 -44.20 -138.94 REMARK 500 2 SER A 113 145.73 -173.19 REMARK 500 3 TYR A 60 -47.78 -135.36 REMARK 500 3 PHE A 100 -17.14 -142.56 REMARK 500 4 TYR A 60 -52.95 -131.15 REMARK 500 4 LYS A 70 -164.36 -124.60 REMARK 500 4 PHE A 100 -9.85 -140.01 REMARK 500 4 HIS A 109 -14.18 -143.21 REMARK 500 5 TRP A 61 -36.64 -144.56 REMARK 500 5 PHE A 100 -11.21 -142.03 REMARK 500 6 TYR A 60 -48.59 -136.90 REMARK 500 6 TRP A 106 -63.00 -93.45 REMARK 500 7 TYR A 60 -42.73 -130.19 REMARK 500 7 TRP A 61 -36.76 -144.58 REMARK 500 7 PHE A 100 -1.86 -141.60 REMARK 500 7 HIS A 109 -45.86 -133.23 REMARK 500 8 TYR A 60 -58.25 -132.64 REMARK 500 8 PHE A 100 -6.53 -143.44 REMARK 500 8 TRP A 106 -70.65 -79.75 REMARK 500 8 HIS A 109 -44.55 -138.72 REMARK 500 9 TRP A 61 -42.80 -137.50 REMARK 500 9 PHE A 100 -18.17 -143.60 REMARK 500 10 TRP A 61 -55.83 -138.78 REMARK 500 10 LYS A 70 -165.53 -127.92 REMARK 500 10 PHE A 100 -3.54 -141.93 REMARK 500 10 HIS A 109 -45.96 -137.21 REMARK 500 11 TYR A 60 -61.85 -130.65 REMARK 500 11 LYS A 70 -168.87 -119.01 REMARK 500 11 PHE A 100 -4.42 -144.46 REMARK 500 12 TRP A 61 -56.89 -138.47 REMARK 500 12 LYS A 70 -168.86 -121.90 REMARK 500 12 PHE A 100 -4.83 -140.70 REMARK 500 13 TYR A 60 -59.41 -131.00 REMARK 500 13 LYS A 70 -168.91 -119.34 REMARK 500 14 ARG A 36 32.01 71.08 REMARK 500 14 TYR A 60 -35.17 -131.60 REMARK 500 14 TRP A 61 -40.17 -139.67 REMARK 500 14 PHE A 100 -16.48 -142.93 REMARK 500 15 GLU A 33 -60.26 -94.58 REMARK 500 15 TRP A 61 -37.30 -134.35 REMARK 500 15 PHE A 100 -3.57 -145.69 REMARK 500 15 HIS A 109 -45.54 -131.72 REMARK 500 16 TYR A 60 -39.31 -132.55 REMARK 500 16 TRP A 61 -40.59 -144.29 REMARK 500 16 PHE A 100 -13.40 -143.84 REMARK 500 REMARK 500 THIS ENTRY HAS 68 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 11468 RELATED DB: BMRB DBREF 2RSC A 2 120 UNP P48816 LYS_BOMMO 19 137 SEQADV 2RSC GLY A 1 UNP P48816 EXPRESSION TAG SEQRES 1 A 120 GLY LYS THR PHE THR ARG CYS GLY LEU VAL HIS GLU LEU SEQRES 2 A 120 ARG LYS HIS GLY PHE GLU GLU ASN LEU MET ARG ASN TRP SEQRES 3 A 120 VAL CYS LEU VAL GLU HIS GLU SER SER ARG ASP THR SER SEQRES 4 A 120 LYS THR ASN THR ASN ARG ASN GLY SER LYS ASP TYR GLY SEQRES 5 A 120 LEU PHE GLN ILE ASN ASP ARG TYR TRP CYS SER LYS GLY SEQRES 6 A 120 ALA SER PRO GLY LYS ASP CYS ASN VAL LYS CYS SER ASP SEQRES 7 A 120 LEU LEU THR ASP ASP ILE THR LYS ALA ALA LYS CYS ALA SEQRES 8 A 120 LYS LYS ILE TYR LYS ARG HIS ARG PHE ASP ALA TRP TYR SEQRES 9 A 120 GLY TRP LYS ASN HIS CYS GLN GLY SER LEU PRO ASP ILE SEQRES 10 A 120 SER SER CYS HELIX 1 1 THR A 5 HIS A 16 1 12 HELIX 2 2 LEU A 22 SER A 34 1 13 HELIX 3 3 SER A 77 THR A 81 5 5 HELIX 4 4 ILE A 84 LYS A 96 1 13 HELIX 5 5 TRP A 103 HIS A 109 1 7 SHEET 1 A 3 THR A 41 THR A 43 0 SHEET 2 A 3 LYS A 49 TYR A 51 -1 O ASP A 50 N ASN A 42 SHEET 3 A 3 ILE A 56 ASN A 57 -1 O ILE A 56 N TYR A 51 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1