HEADER LIPID TRANSPORT 28-JUN-05 2CX7 TITLE CRYSTAL STRUCTURE OF STEROL CARRIER PROTEIN 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: STEROL CARRIER PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS STEROL TRANSFER, SCP-2, RSGI, STRUCTURAL GENOMICS, NPPSFA, NATIONAL KEYWDS 2 PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR K.MURAYAMA,M.SHIROUZU,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 3 23-OCT-24 2CX7 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2CX7 1 VERSN REVDAT 1 28-DEC-05 2CX7 0 JRNL AUTH K.MURAYAMA,M.SHIROUZU,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF STEROL CARRIER PROTEIN 2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1293868.530 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 23313 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1127 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3486 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 179 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1974 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.61000 REMARK 3 B22 (A**2) : -5.33000 REMARK 3 B33 (A**2) : -2.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.530 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.290 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.090 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.460 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 52.34 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CX7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000024727. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790, 0.9793, 0.964 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23346 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 22.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29800 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG4000, 0.2M AMMONIUM SULPHATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 25.24250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.32800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.25600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.32800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.24250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.25600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 MSE A 1 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 ASP A 40 81.72 -151.06 REMARK 500 TYR B 115 40.21 -107.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003001886.2 RELATED DB: TARGETDB DBREF 2CX7 A 1 130 UNP Q5SL92 Q5SL92_THET8 1 130 DBREF 2CX7 B 1 130 UNP Q5SL92 Q5SL92_THET8 1 130 SEQADV 2CX7 MSE A 1 UNP Q5SL92 MET 1 MODIFIED RESIDUE SEQADV 2CX7 MSE A 98 UNP Q5SL92 MET 98 MODIFIED RESIDUE SEQADV 2CX7 MSE B 1 UNP Q5SL92 MET 1 MODIFIED RESIDUE SEQADV 2CX7 MSE B 98 UNP Q5SL92 MET 98 MODIFIED RESIDUE SEQRES 1 A 130 MSE GLU LEU PHE THR GLU ALA TRP ALA GLN ALA TYR CYS SEQRES 2 A 130 ARG LYS LEU ASN GLU SER GLU ALA TYR ARG LYS ALA ALA SEQRES 3 A 130 SER THR TRP GLU GLY SER LEU ALA LEU ALA VAL ARG PRO SEQRES 4 A 130 ASP PRO LYS ALA GLY PHE PRO LYS GLY VAL ALA VAL VAL SEQRES 5 A 130 LEU ASP LEU TRP HIS GLY ALA CYS ARG GLY ALA LYS ALA SEQRES 6 A 130 VAL GLU GLY GLU ALA GLU ALA ASP PHE VAL ILE GLU ALA SEQRES 7 A 130 ASP LEU ALA THR TRP GLN GLU VAL LEU GLU GLY ARG LEU SEQRES 8 A 130 GLU PRO LEU SER ALA LEU MSE ARG GLY LEU LEU GLU LEU SEQRES 9 A 130 LYS LYS GLY THR ILE ALA ALA LEU ALA PRO TYR ALA GLN SEQRES 10 A 130 ALA ALA GLN GLU LEU VAL LYS VAL ALA ARG GLU VAL ALA SEQRES 1 B 130 MSE GLU LEU PHE THR GLU ALA TRP ALA GLN ALA TYR CYS SEQRES 2 B 130 ARG LYS LEU ASN GLU SER GLU ALA TYR ARG LYS ALA ALA SEQRES 3 B 130 SER THR TRP GLU GLY SER LEU ALA LEU ALA VAL ARG PRO SEQRES 4 B 130 ASP PRO LYS ALA GLY PHE PRO LYS GLY VAL ALA VAL VAL SEQRES 5 B 130 LEU ASP LEU TRP HIS GLY ALA CYS ARG GLY ALA LYS ALA SEQRES 6 B 130 VAL GLU GLY GLU ALA GLU ALA ASP PHE VAL ILE GLU ALA SEQRES 7 B 130 ASP LEU ALA THR TRP GLN GLU VAL LEU GLU GLY ARG LEU SEQRES 8 B 130 GLU PRO LEU SER ALA LEU MSE ARG GLY LEU LEU GLU LEU SEQRES 9 B 130 LYS LYS GLY THR ILE ALA ALA LEU ALA PRO TYR ALA GLN SEQRES 10 B 130 ALA ALA GLN GLU LEU VAL LYS VAL ALA ARG GLU VAL ALA MODRES 2CX7 MSE A 98 MET SELENOMETHIONINE MODRES 2CX7 MSE B 1 MET SELENOMETHIONINE MODRES 2CX7 MSE B 98 MET SELENOMETHIONINE HET MSE A 98 8 HET MSE B 1 8 HET MSE B 98 8 HET PO4 B1001 5 HETNAM MSE SELENOMETHIONINE HETNAM PO4 PHOSPHATE ION FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *310(H2 O) HELIX 1 1 THR A 5 GLU A 18 1 14 HELIX 2 2 SER A 19 ALA A 26 1 8 HELIX 3 3 ASP A 40 GLY A 44 5 5 HELIX 4 4 ASP A 79 LEU A 87 1 9 HELIX 5 5 GLU A 92 ARG A 99 1 8 HELIX 6 6 THR A 108 ALA A 113 1 6 HELIX 7 7 TYR A 115 GLU A 128 1 14 HELIX 8 8 THR B 5 SER B 19 1 15 HELIX 9 9 SER B 19 ALA B 26 1 8 HELIX 10 10 ASP B 40 GLY B 44 5 5 HELIX 11 11 ASP B 79 GLY B 89 1 11 HELIX 12 12 GLU B 92 ARG B 99 1 8 HELIX 13 13 THR B 108 ALA B 113 1 6 HELIX 14 14 TYR B 115 ALA B 130 1 16 SHEET 1 A 5 ALA A 59 GLU A 67 0 SHEET 2 A 5 VAL A 49 TRP A 56 -1 N ASP A 54 O GLY A 62 SHEET 3 A 5 GLU A 30 VAL A 37 -1 N VAL A 37 O VAL A 49 SHEET 4 A 5 PHE A 74 ALA A 78 1 O ILE A 76 N ALA A 36 SHEET 5 A 5 GLU A 103 LYS A 106 -1 O GLU A 103 N GLU A 77 SHEET 1 B 5 ALA B 59 GLU B 67 0 SHEET 2 B 5 VAL B 49 TRP B 56 -1 N VAL B 52 O LYS B 64 SHEET 3 B 5 GLU B 30 VAL B 37 -1 N VAL B 37 O VAL B 49 SHEET 4 B 5 PHE B 74 ALA B 78 1 O ILE B 76 N ALA B 36 SHEET 5 B 5 GLU B 103 LYS B 106 -1 O GLU B 103 N GLU B 77 SSBOND 1 CYS A 13 CYS A 60 1555 1555 2.05 SSBOND 2 CYS B 13 CYS B 60 1555 1555 2.06 LINK C LEU A 97 N MSE A 98 1555 1555 1.33 LINK C MSE A 98 N ARG A 99 1555 1555 1.33 LINK C MSE B 1 N GLU B 2 1555 1555 1.33 LINK C LEU B 97 N MSE B 98 1555 1555 1.33 LINK C MSE B 98 N ARG B 99 1555 1555 1.33 SITE 1 AC1 4 GLU A 20 ARG A 23 GLU B 77 GLU B 103 CRYST1 50.485 64.512 70.656 90.00 90.00 90.00 P 21 21 21 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 0.019808 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015501 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014153 0.00000