HEADER SUGAR BINDING PROTEIN 04-JUL-05 2A6Z TITLE CRYSTAL STRUCTURE OF EMP47P CARBOHYDRATE RECOGNITION DOMAIN (CRD), TITLE 2 MONOCLINIC CRYSTAL FORM 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EMP47P (FORM2); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 7-227; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX4T-1 KEYWDS BETA SANDWICH, CARBOHYDRATE BINDING PROTEIN, CARGO RECEPTOR, KEYWDS 2 STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 3 AND FUNCTIONAL ANALYSES, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.SATOH,K.SATO,A.KANOH,K.YAMASHITA,R.KATO,A.NAKANO,S.WAKATSUKI REVDAT 5 09-OCT-24 2A6Z 1 REMARK REVDAT 4 25-OCT-23 2A6Z 1 SEQADV REVDAT 3 24-FEB-09 2A6Z 1 VERSN REVDAT 2 23-MAY-06 2A6Z 1 JRNL REVDAT 1 31-JAN-06 2A6Z 0 JRNL AUTH T.SATOH,K.SATO,A.KANOH,K.YAMASHITA,Y.YAMADA,N.IGARASHI, JRNL AUTH 2 R.KATO,A.NAKANO,S.WAKATSUKI JRNL TITL STRUCTURES OF THE CARBOHYDRATE RECOGNITION DOMAIN OF JRNL TITL 2 CA2+-INDEPENDENT CARGO RECEPTORS EMP46P AND EMP47P. JRNL REF J.BIOL.CHEM. V. 281 10410 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16439369 JRNL DOI 10.1074/JBC.M512258200 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.130 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.130 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 4953 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 94223 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.123 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 4491 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 85243 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1749 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 320 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2068.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 10 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 18836 REMARK 3 NUMBER OF RESTRAINTS : 22535 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.031 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.092 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.112 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.030 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.045 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.090 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2A6Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000033565. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9779 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 99298 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.24900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2A6Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, AMMONIUM CHLORIDE, PH 6.3, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z 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 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 1.000000 0.000000 0.000000 36.26000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.49500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.26000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.49500 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 256 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 88 CB SER A 88 OG -0.080 REMARK 500 MET A 153 CG MET A 153 SD -0.173 REMARK 500 REMARK 500 REMARK: NULL 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 MET A 70 CA - CB - CG ANGL. DEV. = 10.6 DEGREES REMARK 500 ARG A 99 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP A 145 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP A 181 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP A 181 CB - CG - OD2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ARG A 192 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 199 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 199 NE - CZ - NH2 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 GLU A 35 -130.00 59.09 REMARK 500 GLU A 41 100.00 -58.42 REMARK 500 TYR A 155 -23.12 -140.07 REMARK 500 ASN A 182 -1.31 76.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GV9 RELATED DB: PDB REMARK 900 RELATED ID: 1R1Z RELATED DB: PDB REMARK 900 RELATED ID: 2A6V RELATED DB: PDB REMARK 900 RELATED ID: 2A6W RELATED DB: PDB REMARK 900 RELATED ID: 2A6X RELATED DB: PDB REMARK 900 RELATED ID: 2A6Y RELATED DB: PDB REMARK 900 RELATED ID: 2A70 RELATED DB: PDB REMARK 900 RELATED ID: 2A71 RELATED DB: PDB DBREF 2A6Z A 7 227 GB 854516 CAA60953 35 255 SEQADV 2A6Z GLY A 6 GB 854516 CLONING ARTIFACT SEQRES 1 A 222 GLY SER ASP ALA SER LYS LEU SER SER ASP TYR SER LEU SEQRES 2 A 222 PRO ASP LEU ILE ASN THR ARG LYS VAL PRO ASN ASN TRP SEQRES 3 A 222 GLN THR GLY GLU GLN ALA SER LEU GLU GLU GLY ARG ILE SEQRES 4 A 222 VAL LEU THR SER ASN GLN ASN SER LYS GLY SER LEU TRP SEQRES 5 A 222 LEU LYS GLN GLY PHE ASP LEU LYS ASP SER PHE THR MET SEQRES 6 A 222 GLU TRP THR PHE ARG SER VAL GLY TYR SER GLY GLN THR SEQRES 7 A 222 ASP GLY GLY ILE SER PHE TRP PHE VAL GLN ASP SER ASN SEQRES 8 A 222 ILE PRO ARG ASP LYS GLN LEU TYR ASN GLY PRO VAL ASN SEQRES 9 A 222 TYR ASP GLY LEU GLN LEU LEU VAL ASP ASN ASN GLY PRO SEQRES 10 A 222 LEU GLY PRO THR LEU ARG GLY GLN LEU ASN ASP GLY GLN SEQRES 11 A 222 LYS PRO VAL ASP LYS THR LYS ILE TYR ASP GLN SER PHE SEQRES 12 A 222 ALA SER CYS LEU MET GLY TYR GLN ASP SER SER VAL PRO SEQRES 13 A 222 SER THR ILE ARG VAL THR TYR ASP LEU GLU ASP ASP ASN SEQRES 14 A 222 LEU LEU LYS VAL GLN VAL ASP ASN LYS VAL CYS PHE GLN SEQRES 15 A 222 THR ARG LYS VAL ARG PHE PRO SER GLY SER TYR ARG ILE SEQRES 16 A 222 GLY VAL THR ALA GLN ASN GLY ALA VAL ASN ASN ASN ALA SEQRES 17 A 222 GLU SER PHE GLU ILE PHE LYS MET GLN PHE PHE ASN GLY SEQRES 18 A 222 VAL FORMUL 2 HOH *320(H2 O) HELIX 1 1 SER A 14 SER A 17 5 4 HELIX 2 2 ILE A 143 SER A 147 1 5 SHEET 1 A 7 TRP A 31 GLU A 35 0 SHEET 2 A 7 LYS A 53 LEU A 58 -1 O TRP A 57 N GLN A 32 SHEET 3 A 7 TYR A 198 GLN A 205 -1 O ALA A 204 N GLY A 54 SHEET 4 A 7 GLY A 86 GLN A 93 -1 N VAL A 92 O ARG A 199 SHEET 5 A 7 ASP A 111 ASP A 118 -1 O ASP A 111 N GLN A 93 SHEET 6 A 7 THR A 126 ASP A 133 -1 O ARG A 128 N LEU A 116 SHEET 7 A 7 ALA A 149 LEU A 152 -1 O ALA A 149 N GLY A 129 SHEET 1 B 7 SER A 38 GLU A 40 0 SHEET 2 B 7 ARG A 43 VAL A 45 -1 O VAL A 45 N SER A 38 SHEET 3 B 7 SER A 215 ASN A 225 -1 O ILE A 218 N ILE A 44 SHEET 4 B 7 PHE A 68 VAL A 77 -1 N ARG A 75 O GLU A 217 SHEET 5 B 7 SER A 162 ASP A 169 -1 O SER A 162 N PHE A 74 SHEET 6 B 7 LEU A 175 VAL A 180 -1 O LYS A 177 N THR A 167 SHEET 7 B 7 LYS A 183 THR A 188 -1 O THR A 188 N LEU A 176 SSBOND 1 CYS A 151 CYS A 185 1555 1555 2.06 CRYST1 72.520 64.990 41.540 90.00 96.68 90.00 C 1 2 1 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 0.013789 0.000000 0.001615 0.00000 SCALE2 0.000000 0.015388 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024241 0.00000