HEADER SUGAR BINDING PROTEIN 22-JUN-04 1WLD TITLE CONGERIN II T88I SINGLE MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONGERIN II; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-GALACTOSIDE-BINDING LECTIN 2; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CONGER MYRIASTER; SOURCE 3 ORGANISM_COMMON: WHITESPOTTED CONGER; SOURCE 4 ORGANISM_TAXID: 7943; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PTV118N KEYWDS GALECTIN, BETA-SANDWICH, THERMOSTABILITY, MUTANT, SUGAR BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.SHIONYU-MITSUYAMA,Y.ITO,A.KONNO,Y.MIWA,T.OGAWA,K.MURAMOTO,T.SHIRAI REVDAT 5 10-NOV-21 1WLD 1 SEQADV HETSYN REVDAT 4 29-JUL-20 1WLD 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 04-AUG-09 1WLD 1 FORMUL HET HETATM HETNAM REVDAT 3 2 1 LINK SITE REVDAT 2 24-FEB-09 1WLD 1 VERSN REVDAT 1 07-JUN-05 1WLD 0 JRNL AUTH C.SHIONYU-MITSUYAMA,Y.ITO,A.KONNO,Y.MIWA,T.OGAWA,K.MURAMOTO, JRNL AUTH 2 T.SHIRAI JRNL TITL IN VITRO EVOLUTIONARY THERMOSTABILIZATION OF CONGERIN II: A JRNL TITL 2 LIMITED REPRODUCTION OF NATURAL PROTEIN EVOLUTION BY JRNL TITL 3 ARTIFICIAL SELECTION PRESSURE JRNL REF J.MOL.BIOL. V. 347 385 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15740748 JRNL DOI 10.1016/J.JMB.2005.01.027 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 18572 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 999 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1079 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 148 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 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 1WLD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000023703. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19825 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04900 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8M MAGNESIUM SULFATE, 0.93MM REMARK 280 LACTOSE, 0.05M MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.48500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.48500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.95500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.48500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.48500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.95500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.48500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.48500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 39.95500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.48500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.48500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.95500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: DIMERIC 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 79.91000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 1 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 3 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 3 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 48 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 74 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ASP A 93 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 112 NE - CZ - NH1 ANGL. DEV. = 3.5 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 VAL A 67 -53.21 -131.59 REMARK 500 GLN A 70 -146.76 -91.75 REMARK 500 PHE A 78 68.83 -152.88 REMARK 500 ASP A 93 -167.69 -120.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WLC RELATED DB: PDB REMARK 900 CONGERIN II Y16S/T88I DOUBLE MUTANT REMARK 900 RELATED ID: 1IS3 RELATED DB: PDB REMARK 900 STRUCTURE OF WILD TYPE CONGERIN II DBREF 1WLD A 1 135 UNP Q9YIC2 LEG2_CONMY 1 135 SEQADV 1WLD ILE A 88 UNP Q9YIC2 THR 88 ENGINEERED MUTATION SEQRES 1 A 135 SER ASP ARG ALA GLU VAL ARG ASN ILE PRO PHE LYS LEU SEQRES 2 A 135 GLY MET TYR LEU THR VAL GLY GLY VAL VAL ASN SER ASN SEQRES 3 A 135 ALA THR ARG PHE SER ILE ASN VAL GLY GLU SER THR ASP SEQRES 4 A 135 SER ILE ALA MET HIS MET ASP HIS ARG PHE SER TYR GLY SEQRES 5 A 135 ALA ASP GLN ASN VAL LEU VAL LEU ASN SER LEU VAL HIS SEQRES 6 A 135 ASN VAL GLY TRP GLN GLN GLU GLU ARG SER LYS LYS PHE SEQRES 7 A 135 PRO PHE THR LYS GLY ASP HIS PHE GLN ILE THR ILE THR SEQRES 8 A 135 PHE ASP THR HIS THR PHE TYR ILE GLN LEU SER ASN GLY SEQRES 9 A 135 GLU THR VAL GLU PHE PRO ASN ARG ASN LYS ASP ALA ALA SEQRES 10 A 135 PHE ASN LEU ILE TYR LEU ALA GLY ASP ALA ARG LEU THR SEQRES 11 A 135 PHE VAL ARG LEU GLU HET BGC B 1 12 HET GAL B 2 11 HET MES A 777 12 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 2 BGC C6 H12 O6 FORMUL 2 GAL C6 H12 O6 FORMUL 3 MES C6 H13 N O4 S FORMUL 4 HOH *148(H2 O) SHEET 1 A 6 ALA A 4 LYS A 12 0 SHEET 2 A 6 ALA A 117 GLY A 125 -1 O ASN A 119 N ASN A 8 SHEET 3 A 6 ARG A 29 SER A 37 -1 N GLY A 35 O LEU A 120 SHEET 4 A 6 SER A 40 TYR A 51 -1 O HIS A 47 N PHE A 30 SHEET 5 A 6 ASP A 54 VAL A 64 -1 O VAL A 59 N ASP A 46 SHEET 6 A 6 GLY A 68 TRP A 69 -1 O GLY A 68 N VAL A 64 SHEET 1 B 6 ALA A 4 LYS A 12 0 SHEET 2 B 6 ALA A 117 GLY A 125 -1 O ASN A 119 N ASN A 8 SHEET 3 B 6 ARG A 29 SER A 37 -1 N GLY A 35 O LEU A 120 SHEET 4 B 6 SER A 40 TYR A 51 -1 O HIS A 47 N PHE A 30 SHEET 5 B 6 ASP A 54 VAL A 64 -1 O VAL A 59 N ASP A 46 SHEET 6 B 6 GLU A 73 SER A 75 -1 O GLU A 73 N LEU A 60 SHEET 1 C 5 THR A 106 PRO A 110 0 SHEET 2 C 5 THR A 96 GLN A 100 -1 N PHE A 97 O PHE A 109 SHEET 3 C 5 HIS A 85 PHE A 92 -1 N THR A 91 O TYR A 98 SHEET 4 C 5 LEU A 17 VAL A 23 -1 N LEU A 17 O ILE A 90 SHEET 5 C 5 ALA A 127 LEU A 134 -1 O ARG A 133 N THR A 18 LINK O4 BGC B 1 C1 GAL B 2 1555 1555 1.41 CRYST1 60.970 60.970 79.910 90.00 90.00 90.00 P 42 21 2 8 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 0.016402 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012514 0.00000