HEADER RETINOIC-ACID TRANSPORT 12-JUL-95 1CBI TITLE APO-CELLULAR RETINOIC ACID BINDING PROTEIN I COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR RETINOIC ACID BINDING PROTEIN I; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: APO FORM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MOUSE CRABPI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMON2670; SOURCE 9 EXPRESSION_SYSTEM_GENE: MOUSE CRABPI KEYWDS RETINOIC-ACID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.R.THOMPSON,J.M.BRATT,L.J.BANASZAK REVDAT 5 07-FEB-24 1CBI 1 REMARK REVDAT 4 29-NOV-17 1CBI 1 HELIX REVDAT 3 24-FEB-09 1CBI 1 VERSN REVDAT 2 30-SEP-03 1CBI 1 DBREF REVDAT 1 14-NOV-95 1CBI 0 JRNL AUTH J.R.THOMPSON,J.M.BRATT,L.J.BANASZAK JRNL TITL CRYSTAL STRUCTURE OF CELLULAR RETINOIC ACID BINDING PROTEIN JRNL TITL 2 I SHOWS INCREASED ACCESS TO THE BINDING CAVITY DUE TO JRNL TITL 3 FORMATION OF AN INTERMOLECULAR BETA-SHEET. JRNL REF J.MOL.BIOL. V. 252 433 1995 JRNL REFN ISSN 0022-2836 JRNL PMID 7563063 JRNL DOI 10.1006/JMBI.1995.0509 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.J.KLEYWEGT,T.BERGFORS,H.SENN,P.LE MOTTE,B.GSELL,K.SHUDO, REMARK 1 AUTH 2 A.T.JONES REMARK 1 TITL CRYSTAL STRUCTURES OF CELLULAR RETINOIC ACID BINDING REMARK 1 TITL 2 PROTEINS I AND II IN COMPLEX WITH ALL-TRANS-RETINOIC ACID REMARK 1 TITL 3 AND A SYNTHETIC RETINOID REMARK 1 REF STRUCTURE V. 2 1241 1994 REMARK 1 REFN ISSN 0969-2126 REMARK 2 REMARK 2 RESOLUTION. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11857 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) : 0.196 REMARK 3 FREE R VALUE : 0.233 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL 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 : 2174 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 71 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.00 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) : 0.30 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.560 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.210 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: NULL REMARK 4 REMARK 4 1CBI 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_1000172208. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-93 REMARK 200 TEMPERATURE (KELVIN) : 294 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12365 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 200 DATA REDUNDANCY : 23.00 REMARK 200 R MERGE (I) : 0.10900 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.86667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.73333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.73333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 17.86667 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 300 REMARK: MTRIX REMARK 300 THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW REMARK 300 DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE REMARK 300 VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE REMARK 300 MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL REMARK 300 YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED REMARK 300 SECOND. REMARK 300 APPLIED TO TRANSFORMED TO REMARK 300 MTRIX RESIDUES RESIDUES RMSD 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 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 ASN A 2 -163.68 -114.72 REMARK 500 THR A 56 -134.13 -150.77 REMARK 500 VAL A 58 -3.16 -146.18 REMARK 500 GLU A 73 -147.70 -157.66 REMARK 500 ASP A 125 -124.46 75.90 REMARK 500 GLU B 73 -160.95 -162.22 REMARK 500 ASP B 103 113.90 79.88 REMARK 500 ASP B 125 -122.41 62.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 CRABPI IS ACTUALLY A TEN-STRANDED BETA-BARREL. THIS IS REMARK 700 REPRESENTED IN SHEET RECORDS BELOW BY AN ELEVEN-STRANDED REMARK 700 SHEET. DBREF 1CBI A 1 136 UNP P62965 RABP1_MOUSE 1 136 DBREF 1CBI B 1 136 UNP P62965 RABP1_MOUSE 1 136 SEQRES 1 A 136 PRO ASN PHE ALA GLY THR TRP LYS MET ARG SER SER GLU SEQRES 2 A 136 ASN PHE ASP GLU LEU LEU LYS ALA LEU GLY VAL ASN ALA SEQRES 3 A 136 MET LEU ARG LYS VAL ALA VAL ALA ALA ALA SER LYS PRO SEQRES 4 A 136 HIS VAL GLU ILE ARG GLN ASP GLY ASP GLN PHE TYR ILE SEQRES 5 A 136 LYS THR SER THR THR VAL ARG THR THR GLU ILE ASN PHE SEQRES 6 A 136 LYS VAL GLY GLU GLY PHE GLU GLU GLU THR VAL ASP GLY SEQRES 7 A 136 ARG LYS CYS ARG SER LEU PRO THR TRP GLU ASN GLU ASN SEQRES 8 A 136 LYS ILE HIS CYS THR GLN THR LEU LEU GLU GLY ASP GLY SEQRES 9 A 136 PRO LYS THR TYR TRP THR ARG GLU LEU ALA ASN ASP GLU SEQRES 10 A 136 LEU ILE LEU THR PHE GLY ALA ASP ASP VAL VAL CYS THR SEQRES 11 A 136 ARG ILE TYR VAL ARG GLU SEQRES 1 B 136 PRO ASN PHE ALA GLY THR TRP LYS MET ARG SER SER GLU SEQRES 2 B 136 ASN PHE ASP GLU LEU LEU LYS ALA LEU GLY VAL ASN ALA SEQRES 3 B 136 MET LEU ARG LYS VAL ALA VAL ALA ALA ALA SER LYS PRO SEQRES 4 B 136 HIS VAL GLU ILE ARG GLN ASP GLY ASP GLN PHE TYR ILE SEQRES 5 B 136 LYS THR SER THR THR VAL ARG THR THR GLU ILE ASN PHE SEQRES 6 B 136 LYS VAL GLY GLU GLY PHE GLU GLU GLU THR VAL ASP GLY SEQRES 7 B 136 ARG LYS CYS ARG SER LEU PRO THR TRP GLU ASN GLU ASN SEQRES 8 B 136 LYS ILE HIS CYS THR GLN THR LEU LEU GLU GLY ASP GLY SEQRES 9 B 136 PRO LYS THR TYR TRP THR ARG GLU LEU ALA ASN ASP GLU SEQRES 10 B 136 LEU ILE LEU THR PHE GLY ALA ASP ASP VAL VAL CYS THR SEQRES 11 B 136 ARG ILE TYR VAL ARG GLU FORMUL 3 HOH *71(H2 O) HELIX 1 H1A PHE A 15 ALA A 21 1 7 HELIX 2 H2A ALA A 26 SER A 37 1 12 HELIX 3 H1B PHE B 15 ALA B 21 1 7 HELIX 4 H2B ALA B 26 SER B 37 1 12 SHEET 1 A11 GLY A 5 GLU A 13 0 SHEET 2 A11 HIS A 40 ASP A 46 -1 O VAL A 41 N TRP A 7 SHEET 3 A11 GLN A 49 SER A 55 -1 O GLN A 49 N ASP A 46 SHEET 4 A11 THR A 60 LYS A 66 -1 O THR A 61 N THR A 54 SHEET 5 A11 PHE A 71 GLU A 74 -1 SHEET 6 A11 LYS A 80 ASN A 89 -1 O CYS A 81 N GLU A 73 SHEET 7 A11 LYS A 92 LEU A 99 -1 O LYS A 92 N ASN A 89 SHEET 8 A11 THR A 107 ALA A 114 -1 O TRP A 109 N CYS A 95 SHEET 9 A11 GLU A 117 ALA A 124 -1 O GLU A 117 N ALA A 114 SHEET 10 A11 VAL A 127 ARG A 135 -1 O VAL A 127 N ALA A 124 SHEET 11 A11 GLY A 5 GLU A 13 -1 O LYS A 8 N VAL A 134 SHEET 1 B11 GLY B 5 GLU B 13 0 SHEET 2 B11 HIS B 40 ASP B 46 -1 O VAL B 41 N TRP B 7 SHEET 3 B11 GLN B 49 SER B 55 -1 O GLN B 49 N ASP B 46 SHEET 4 B11 THR B 60 LYS B 66 -1 O THR B 61 N THR B 54 SHEET 5 B11 PHE B 71 GLU B 74 -1 SHEET 6 B11 LYS B 80 ASN B 89 -1 O CYS B 81 N GLU B 73 SHEET 7 B11 LYS B 92 LEU B 99 -1 O LYS B 92 N ASN B 89 SHEET 8 B11 THR B 107 ALA B 114 -1 O TRP B 109 N CYS B 95 SHEET 9 B11 GLU B 117 ALA B 124 -1 O GLU B 117 N ALA B 114 SHEET 10 B11 VAL B 127 ARG B 135 -1 O VAL B 127 N ALA B 124 SHEET 11 B11 GLY B 5 GLU B 13 -1 O LYS B 8 N VAL B 134 CRYST1 127.450 127.450 53.600 90.00 90.00 120.00 P 31 2 1 12 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 0.007846 0.004530 0.000000 0.00000 SCALE2 0.000000 0.009060 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018657 0.00000 MTRIX1 1 0.872200 -0.486700 0.049500 34.04710 1 MTRIX2 1 -0.488900 -0.870900 0.050100 134.78799 1 MTRIX3 1 0.018700 -0.067900 -0.997500 55.72980 1