HEADER HYDROLASE (O-GLYCOSYL) 13-JAN-95 1LMT TITLE STRUCTURE OF A CONFORMATIONALLY CONSTRAINED ARG-GLY-ASP SEQUENCE TITLE 2 INSERTED INTO HUMAN LYSOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.17; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS HYDROLASE (O-GLYCOSYL) EXPDTA X-RAY DIFFRACTION AUTHOR M.MATSUSHIMA,H.SONG REVDAT 7 29-JUL-20 1LMT 1 COMPND REMARK SEQADV HETNAM REVDAT 7 2 1 LINK SITE ATOM REVDAT 6 14-AUG-19 1LMT 1 REMARK REVDAT 5 17-JUL-19 1LMT 1 REMARK LINK REVDAT 4 29-NOV-17 1LMT 1 HELIX REVDAT 3 13-JUL-11 1LMT 1 VERSN REVDAT 2 24-FEB-09 1LMT 1 VERSN REVDAT 1 31-MAR-95 1LMT 0 JRNL AUTH T.YAMADA,H.SONG,K.INAKA,Y.SHIMADA,M.KIKUCHI,M.MATSUSHIMA JRNL TITL STRUCTURE OF A CONFORMATIONALLY CONSTRAINED ARG-GLY-ASP JRNL TITL 2 SEQUENCE INSERTED INTO HUMAN LYSOZYME. JRNL REF J.BIOL.CHEM. V. 270 5687 1995 JRNL REFN ISSN 0021-9258 JRNL PMID 7890692 JRNL DOI 10.1074/JBC.270.11.5687 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.YAMADA,M.MATSUSHIMA,K.INAKA,T.OHKUBO,A.UYEDA,T.MAEDA, REMARK 1 AUTH 2 K.TITANI,K.SEKIGUCHI,M.KIKUCHI REMARK 1 TITL STRUCTURAL AND FUNCTIONAL ANALYSES OF THE ARG-GLY-ASP REMARK 1 TITL 2 SEQUENCE INTRODUCED INTO HUMAN LYSOZYME REMARK 1 REF J.BIOL.CHEM. V. 268 10588 1993 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12583 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1070 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 115 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL 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) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL 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) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LMT 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_1000174766. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 6.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 28.24500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.71000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.73000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 16.71000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.24500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.73000 REMARK 290 SMTRY3 4 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, 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 400 REMARK 400 COMPOUND REMARK 400 THE LYSOZYME MOLECULE BINDS THE SACCHARIDE MOLECULE, REMARK 400 (GLCNAC)3, IN THE BINDING SUBSITES, A, B, AND C. 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 14 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP A 18 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 18 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 21 NE - CZ - NH2 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 41 CD - NE - CZ ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 41 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 50 CD - NE - CZ ANGL. DEV. = 9.8 DEGREES REMARK 500 THR A 52 O - C - N ANGL. DEV. = 10.0 DEGREES REMARK 500 ASP A 53 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ILE A 56 O - C - N ANGL. DEV. = 9.6 DEGREES REMARK 500 ARG A 101 NE - CZ - NH1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 101 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 107 CD - NE - CZ ANGL. DEV. = 11.4 DEGREES REMARK 500 ARG A 115 NE - CZ - NH2 ANGL. DEV. = -4.9 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 69 78.67 -108.42 REMARK 500 THR A 70 111.89 -160.44 REMARK 500 PRO A 71 -91.52 -75.16 REMARK 500 ASN A 75 69.67 -152.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: RGD REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL DBREF 1LMT A 1 124 UNP P00695 LYC_HUMAN 19 142 SEQADV 1LMT CYS A 74A UNP P00695 INSERTION SEQADV 1LMT ARG A 74B UNP P00695 INSERTION SEQADV 1LMT GLY A 74C UNP P00695 INSERTION SEQADV 1LMT ASP A 74D UNP P00695 INSERTION SEQADV 1LMT SER A 74E UNP P00695 INSERTION SEQADV 1LMT CYS A 74F UNP P00695 INSERTION SEQRES 1 A 136 LYS VAL PHE GLU ARG CYS GLU LEU ALA ARG THR LEU LYS SEQRES 2 A 136 ARG LEU GLY MET ASP GLY TYR ARG GLY ILE SER LEU ALA SEQRES 3 A 136 ASN TRP MET CYS LEU ALA LYS TRP GLU SER GLY TYR ASN SEQRES 4 A 136 THR ARG ALA THR ASN TYR ASN ALA GLY ASP ARG SER THR SEQRES 5 A 136 ASP TYR GLY ILE PHE GLN ILE ASN SER ARG TYR TRP CYS SEQRES 6 A 136 ASN ASP GLY LYS THR PRO GLY ALA VAL CYS ARG GLY ASP SEQRES 7 A 136 SER CYS ASN ALA CYS HIS LEU SER CYS SER ALA LEU LEU SEQRES 8 A 136 GLN ASP ASN ILE ALA ASP ALA VAL ALA CYS ALA LYS ARG SEQRES 9 A 136 VAL VAL ARG ASP PRO GLN GLY ILE ARG ALA TRP VAL ALA SEQRES 10 A 136 TRP ARG ASN ARG CYS GLN ASN ARG ASP VAL ARG GLN TYR SEQRES 11 A 136 VAL GLN GLY CYS GLY VAL HET NAG B 1 15 HET NAG B 2 14 HET NAG B 3 14 HET CL A 145 1 HET CL A 146 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CL CHLORIDE ION FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 3 CL 2(CL 1-) FORMUL 5 HOH *115(H2 O) HELIX 1 A ARG A 5 ARG A 14 1 10 HELIX 2 B LEU A 25 GLU A 35 1 11 HELIX 3 E SER A 80 LEU A 85 5 6 HELIX 4 C ALA A 90 VAL A 99 1 10 HELIX 5 D VAL A 110 CYS A 116 1 7 SHEET 1 A 2 LYS A 1 PHE A 3 0 SHEET 2 A 2 TYR A 38 THR A 40 -1 N THR A 40 O LYS A 1 SHEET 1 B 3 ALA A 42 ASN A 46 0 SHEET 2 B 3 SER A 51 GLY A 55 -1 N GLY A 55 O ALA A 42 SHEET 3 B 3 ILE A 59 SER A 61 -1 N SER A 61 O THR A 52 SSBOND 1 CYS A 6 CYS A 128 1555 1555 2.03 SSBOND 2 CYS A 30 CYS A 116 1555 1555 2.05 SSBOND 3 CYS A 65 CYS A 81 1555 1555 2.08 SSBOND 4 CYS A 74A CYS A 74F 1555 1555 2.06 SSBOND 5 CYS A 77 CYS A 95 1555 1555 2.01 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.38 LINK O4 NAG B 2 C1 NAG B 3 1555 1555 1.38 SITE 1 RGD 3 ARG A 74B GLY A 74C ASP A 74D CRYST1 56.490 61.460 33.420 90.00 90.00 90.00 P 21 21 21 4 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 0.017702 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016271 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029922 0.00000