10 20 30 40 50 60 70 80 2MEB - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 02-MAY-98 2MEB
TITLE CHANGES IN CONFORMATIONAL STABILITY OF A SERIES OF MUTANT TITLE 2 HUMAN LYSOZYMES AT CONSTANT POSITIONS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.17; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BAKER'S YEAST; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: AH22R-; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEL125
KEYWDS ENZYME, HYDROLASE, O-GLYCOSYL, ALPHA + BETA, GLYCOSIDASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.FUNAHASHI,K.TAKANO,Y.YAMAGATA,K.YUTANI
REVDAT 3 24-FEB-09 2MEB 1 VERSN REVDAT 2 01-APR-03 2MEB 1 JRNL REVDAT 1 15-JUL-98 2MEB 0
JRNL AUTH J.FUNAHASHI,K.TAKANO,Y.YAMAGATA,K.YUTANI JRNL TITL CONTRIBUTION OF AMINO ACID SUBSTITUTIONS AT TWO JRNL TITL 2 DIFFERENT INTERIOR POSITIONS TO THE CONFORMATIONAL JRNL TITL 3 STABILITY OF HUMAN LYSOZYME JRNL REF PROTEIN ENG. V. 12 841 1999 JRNL REFN ISSN 0269-2139 JRNL PMID 10556244 JRNL DOI 10.1093/PROTEIN/12.10.841
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.YAMAGATA,M.KUBOTA,Y.SUMIKAWA,J.FUNAHASHI, REMARK 1 AUTH 2 K.TAKANO,S.FUJII,K.YUTANI REMARK 1 TITL CONTRIBUTION OF HYDROGEN BONDS TO THE REMARK 1 TITL 2 CONFORMATIONAL STABILITY OF HUMAN LYSOZYME: REMARK 1 TITL 3 CALORIMETRY AND X-RAY ANALYSIS OF SIX TYR-->PHE REMARK 1 TITL 4 MUTANTS REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH K.TAKANO,Y.YAMAGATA,S.FUJII,K.YUTANI REMARK 1 TITL CONTRIBUTION OF THE HYDROPHOBIC EFFECT TO THE REMARK 1 TITL 2 STABILITY OF HUMAN LYSOZYME: CALORIMETRIC STUDIES REMARK 1 TITL 3 AND X-RAY STRUCTURAL ANALYSES OF THE NINE VALINE REMARK 1 TITL 4 TO ALANINE MUTANTS REMARK 1 REF BIOCHEMISTRY V. 36 688 1997 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH K.TAKANO,J.FUNAHASHI,Y.YAMAGATA,S.FUJII,K.YUTANI REMARK 1 TITL CONTRIBUTION OF WATER MOLECULES IN THE INTERIOR OF REMARK 1 TITL 2 A PROTEIN TO THE CONFORMATIONAL STABILITY REMARK 1 REF J.MOL.BIOL. V. 274 132 1997 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 4 REMARK 1 AUTH J.FUNAHASHI,K.TAKANO,K.OGASAHARA,Y.YAMAGATA, REMARK 1 AUTH 2 K.YUTANI REMARK 1 TITL THE STRUCTURE, STABILITY, AND FOLDING PROCESS OF REMARK 1 TITL 2 AMYLOIDOGENIC MUTANT HUMAN LYSOZYME REMARK 1 REF J.BIOCHEM.(TOKYO) V. 120 1216 1996 REMARK 1 REFN ISSN 0021-924X REMARK 1 REFERENCE 5 REMARK 1 AUTH K.TAKANO,K.OGASAHARA,H.KANEDA,Y.YAMAGATA,S.FUJII, REMARK 1 AUTH 2 E.KANAYA,M.KIKUCHI,M.OOBATAKE,K.YUTANI REMARK 1 TITL CONTRIBUTION OF HYDROPHOBIC RESIDUES TO THE REMARK 1 TITL 2 STABILITY OF HUMAN LYSOZYME: CALORIMETRIC STUDIES REMARK 1 TITL 3 AND X-RAY STRUCTURAL ANALYSIS OF THE FIVE REMARK 1 TITL 4 ISOLEUCINE TO VALINE MUTANTS REMARK 1 REF J.MOL.BIOL. V. 254 62 1995 REMARK 1 REFN ISSN 0022-2836
REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 10211 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 SET) : 0.156 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 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1151 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1029 REMARK 3 NUCLEIC ACID ATOMS : NULL REMARK 3 HETEROGEN ATOMS : NULL REMARK 3 SOLVENT ATOMS : 192 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 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.24 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MEAN B VALUE (MAIN CHAIN) = 13.0 REMARK 3 MEAN B VALUE (SIDE-CHAIN) = 17.9
REMARK 4 REMARK 4 2MEB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-DEC-96 REMARK 200 TEMPERATURE (KELVIN) : 283 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS REMARK 200 DATA SCALING SOFTWARE : PROCESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36209 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.03600 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.08600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ISOMORPHOUS METHOD REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: WILD-TYPE OF HUMAN LYSOZYME REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M TO 1.8M NACL, 20MM ACETATE, PH REMARK 280 4.5
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 28.37500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.93500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.51000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 16.93500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.37500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.51000 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 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 140 DISTANCE = 15.44 ANGSTROMS REMARK 525 HOH A 154 DISTANCE = 12.69 ANGSTROMS REMARK 525 HOH A 156 DISTANCE = 15.75 ANGSTROMS REMARK 525 HOH A 200 DISTANCE = 5.37 ANGSTROMS REMARK 525 HOH A 225 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A 308 DISTANCE = 10.61 ANGSTROMS REMARK 525 HOH A 318 DISTANCE = 5.77 ANGSTROMS REMARK 525 HOH A 320 DISTANCE = 10.77 ANGSTROMS REMARK 525 HOH A 339 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A 341 DISTANCE = 5.31 ANGSTROMS REMARK 525 HOH A 379 DISTANCE = 5.06 ANGSTROMS
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 NA A 601 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 154 O REMARK 620 2 SER A 61 O 145.8 REMARK 620 3 CYS A 65 O 108.0 79.8 REMARK 620 4 VAL A 74 O 86.0 121.8 114.7 REMARK 620 5 HOH A 140 O 78.2 70.6 78.9 162.0 REMARK 620 N 1 2 3 4
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 601
DBREF 2MEB A 1 130 UNP P61626 LYSC_HUMAN 19 148
SEQADV 2MEB LEU A 56 UNP P61626 ILE 74 ENGINEERED
SEQRES 1 A 130 LYS VAL PHE GLU ARG CYS GLU LEU ALA ARG THR LEU LYS SEQRES 2 A 130 ARG LEU GLY MET ASP GLY TYR ARG GLY ILE SER LEU ALA SEQRES 3 A 130 ASN TRP MET CYS LEU ALA LYS TRP GLU SER GLY TYR ASN SEQRES 4 A 130 THR ARG ALA THR ASN TYR ASN ALA GLY ASP ARG SER THR SEQRES 5 A 130 ASP TYR GLY LEU PHE GLN ILE ASN SER ARG TYR TRP CYS SEQRES 6 A 130 ASN ASP GLY LYS THR PRO GLY ALA VAL ASN ALA CYS HIS SEQRES 7 A 130 LEU SER CYS SER ALA LEU LEU GLN ASP ASN ILE ALA ASP SEQRES 8 A 130 ALA VAL ALA CYS ALA LYS ARG VAL VAL ARG ASP PRO GLN SEQRES 9 A 130 GLY ILE ARG ALA TRP VAL ALA TRP ARG ASN ARG CYS GLN SEQRES 10 A 130 ASN ARG ASP VAL ARG GLN TYR VAL GLN GLY CYS GLY VAL
HET NA A 601 1
HETNAM NA SODIUM ION
FORMUL 2 NA NA 1+ FORMUL 3 HOH *191(H2 O)
HELIX 1 1 ARG A 5 ARG A 14 1 10 HELIX 2 2 TYR A 20 GLY A 22 5 3 HELIX 3 3 LEU A 25 SER A 36 1 12 HELIX 4 4 CYS A 81 LEU A 85 5 5 HELIX 5 5 ALA A 90 ARG A 101 1 12 HELIX 6 6 GLY A 105 ALA A 108 5 4 HELIX 7 7 VAL A 110 ARG A 115 1 6 HELIX 8 8 ARG A 122 TYR A 124 5 3
SHEET 1 A 2 THR A 43 ASN A 46 0 SHEET 2 A 2 SER A 51 TYR A 54 -1 N ASP A 53 O ASN A 44
SSBOND 1 CYS A 6 CYS A 128 1555 1555 2.03 SSBOND 2 CYS A 30 CYS A 116 1555 1555 2.03 SSBOND 3 CYS A 65 CYS A 81 1555 1555 2.03 SSBOND 4 CYS A 77 CYS A 95 1555 1555 2.03
LINK NA NA A 601 O HOH A 154 1555 1555 2.26 LINK NA NA A 601 O SER A 61 1555 1554 2.13 LINK NA NA A 601 O CYS A 65 1555 1554 2.40 LINK NA NA A 601 O VAL A 74 1555 1554 2.13 LINK NA NA A 601 O HOH A 140 1555 1555 2.71
SITE 1 AC1 6 SER A 61 CYS A 65 ALA A 73 VAL A 74 SITE 2 AC1 6 HOH A 140 HOH A 154
CRYST1 56.750 61.020 33.870 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 0.017621 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016388 0.000000 0.00000
SCALE3 0.000000 0.000000 0.029525 0.00000