PDB Short entry for 2CBS HEADER TRANSPORT PROTEIN 22-FEB-99 2CBS TITLE CELLULAR RETINOIC ACID BINDING PROTEIN II IN COMPLEX WITH A SYNTHETIC TITLE 2 RETINOIC ACID (RO-13 6307) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (CRABP-II); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-1A KEYWDS RETINOIC-ACID TRANSPORT, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.CHAUDHURI,G.J.KLEYWEGT,T.BERGFORS,T.A.JONES REVDAT 5 23-AUG-23 2CBS 1 REMARK REVDAT 4 06-NOV-19 2CBS 1 JRNL REVDAT 3 24-FEB-09 2CBS 1 VERSN REVDAT 2 01-APR-03 2CBS 1 JRNL REVDAT 1 22-DEC-99 2CBS 0 JRNL AUTH B.N.CHAUDHURI,G.J.KLEYWEGT,I.BROUTIN-L'HERMITE,T.BERGFORS, JRNL AUTH 2 H.SENN,P.LE MOTTE,O.PARTOUCHE,T.A.JONES JRNL TITL STRUCTURES OF CELLULAR RETINOIC ACID BINDING PROTEINS I AND JRNL TITL 2 II IN COMPLEX WITH SYNTHETIC RETINOIDS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 55 1850 1999 JRNL REFN ISSN 0907-4449 JRNL PMID 10531482 JRNL DOI 10.1107/S0907444999011026 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 T.A.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 1 PMID 7704533 REMARK 1 DOI 10.1016/S0969-2126(94)00125-1 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.BANASZAK,N.WINTER,Z.XU,D.A.BERNLOHR,S.COWAN,T.A.JONES REMARK 1 TITL LIPID-BINDING PROTEINS: A FAMILY OF FATTY ACID AND RETINOID REMARK 1 TITL 2 TRANSPORT PROTEINS. REMARK 1 REF ADV.PROTEIN CHEM. V. 45 89 1994 REMARK 1 REFN ISSN 0065-3233 REMARK 1 PMID 8154375 REMARK 1 REFERENCE 3 REMARK 1 AUTH T.BERGFORS,G.J.KLEYWEGT,T.A.JONES REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF REMARK 1 TITL 2 RECOMBINANT BOVINE CELLULAR RETINOIC ACID-BINDING PROTEIN. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 50 370 1994 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 15299387 REMARK 1 DOI 10.1107/S0907444994001204 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.3 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 9453 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) : 0.200 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.300 REMARK 3 FREE R VALUE TEST SET COUNT : 780 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1396 REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 117 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1091 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.29000 REMARK 3 B22 (A**2) : -0.64000 REMARK 3 B33 (A**2) : 3.93000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.10 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.690 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) : 1.400 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.190 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.630 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.050 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : R13.PAR REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : R13.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2CBS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-99. REMARK 100 THE DEPOSITION ID IS D_1000000533. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9683 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 45.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.16000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 11.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: 1CBS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% MONOMETHYL PEG 5000 0.1 M SODIUM REMARK 280 ACETATE PH 5.5 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 22.62500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.41500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.82000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.41500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.62500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.82000 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 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 73 -159.44 -148.36 REMARK 500 ASP A 126 -116.51 55.50 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 R13 A 200 DBREF 2CBS A 1 137 UNP P29373 RABP2_HUMAN 2 138 SEQRES 1 A 137 PRO ASN PHE SER GLY ASN TRP LYS ILE ILE ARG SER GLU SEQRES 2 A 137 ASN PHE GLU GLU LEU LEU LYS VAL LEU GLY VAL ASN VAL SEQRES 3 A 137 MET LEU ARG LYS ILE ALA VAL ALA ALA ALA SER LYS PRO SEQRES 4 A 137 ALA VAL GLU ILE LYS GLN GLU GLY ASP THR PHE TYR ILE SEQRES 5 A 137 LYS THR SER THR THR VAL ARG THR THR GLU ILE ASN PHE SEQRES 6 A 137 LYS VAL GLY GLU GLU PHE GLU GLU GLN THR VAL ASP GLY SEQRES 7 A 137 ARG PRO CYS LYS SER LEU VAL LYS TRP GLU SER GLU ASN SEQRES 8 A 137 LYS MET VAL CYS GLU GLN LYS LEU LEU LYS GLY GLU GLY SEQRES 9 A 137 PRO LYS THR SER TRP THR ARG GLU LEU THR ASN ASP GLY SEQRES 10 A 137 GLU LEU ILE LEU THR MET THR ALA ASP ASP VAL VAL CYS SEQRES 11 A 137 THR ARG VAL TYR VAL ARG GLU HET R13 A 200 25 HETNAM R13 3-METHYL-7-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRO- HETNAM 2 R13 NAPHTHALEN-2-YL) -OCTA-2,4,6-TRIENOIC ACID FORMUL 2 R13 C23 H30 O2 FORMUL 3 HOH *53(H2 O) HELIX 1 1 PHE A 15 VAL A 21 1 7 HELIX 2 2 VAL A 26 LYS A 38 1 13 SHEET 1 A10 THR A 60 LYS A 66 0 SHEET 2 A10 THR A 49 SER A 55 -1 N THR A 54 O THR A 61 SHEET 3 A10 ALA A 40 GLU A 46 -1 N GLU A 46 O THR A 49 SHEET 4 A10 GLY A 5 GLU A 13 -1 N TRP A 7 O VAL A 41 SHEET 5 A10 VAL A 128 ARG A 136 -1 N VAL A 135 O LYS A 8 SHEET 6 A10 LEU A 119 ALA A 125 -1 N ALA A 125 O VAL A 128 SHEET 7 A10 THR A 107 LEU A 113 -1 N GLU A 112 O ILE A 120 SHEET 8 A10 LYS A 92 LEU A 99 -1 N CYS A 95 O TRP A 109 SHEET 9 A10 PRO A 80 SER A 89 -1 N SER A 89 O LYS A 92 SHEET 10 A10 PHE A 71 GLN A 74 -1 N GLU A 73 O CYS A 81 SITE 1 AC1 13 ARG A 11 VAL A 24 ALA A 32 THR A 54 SITE 2 AC1 13 THR A 56 VAL A 58 ARG A 59 VAL A 76 SITE 3 AC1 13 LEU A 121 ARG A 132 TYR A 134 HOH A 207 SITE 4 AC1 13 HOH A 227 CRYST1 45.250 47.640 74.830 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 0.022099 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020991 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013364 0.00000