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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
