PDB Short entry for 1LPJ HEADER TRANSPORT PROTEIN 08-MAY-02 1LPJ TITLE HUMAN CRBP IV COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOL-BINDING PROTEIN IV, CELLULAR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CRBP-IV, RETINOID BINDING PROTEIN 7; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CELLULAR RETINOL-BINDING PROTEIN, CRBP, RETINOL, VITAMIN A, ILBPS, KEYWDS 2 TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.CALDERONE,G.ZANOTTI,R.BERNI,C.FOLLI REVDAT 3 16-AUG-23 1LPJ 1 REMARK REVDAT 2 24-FEB-09 1LPJ 1 VERSN REVDAT 1 14-JAN-03 1LPJ 0 JRNL AUTH C.FOLLI,V.CALDERONE,I.RAMAZZINA,G.ZANOTTI,R.BERNI JRNL TITL LIGAND BINDING AND STRUCTURAL ANALYSIS OF A HUMAN PUTATIVE JRNL TITL 2 CELLULAR RETINOL-BINDING PROTEIN JRNL REF J.BIOL.CHEM. V. 277 41970 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 12177003 JRNL DOI 10.1074/JBC.M207124200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.W.COWAN,M.E.NEWCOMER,T.A.JONES REMARK 1 TITL CRYSTALLOGRAPHIC STUDIES ON A FAMILY OF CELLULAR LIPOPHILIC REMARK 1 TITL 2 TRANSPORT PROTEINS. REFINEMENT OF P2 MYELIN PROTEIN AND THE REMARK 1 TITL 3 STRUCTURE DETERMINATION AND REFINEMENT OF CELLULAR REMARK 1 TITL 4 RETINOL-BINDING PROTEIN IN COMPLEX WITH ALL-TRANS-RETINOL. REMARK 1 REF J.MOL.BIOL. V. 230 1225 1993 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1993.1238 REMARK 1 REFERENCE 2 REMARK 1 AUTH N.S.WINTER,J.M.BRATT,L.J.BANASZAK REMARK 1 TITL CRYSTAL STRUCTURES OF HOLO AND APO-CELLULAR RETINOL-BINDING REMARK 1 TITL 2 PROTEIN II REMARK 1 REF J.MOL.BIOL. V. 230 1247 1993 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1993.1239 REMARK 1 REFERENCE 3 REMARK 1 AUTH C.FOLLI,V.CALDERONE,S.OTTONELLO,A.BOLCHI,G.ZANOTTI, REMARK 1 AUTH 2 M.STOPPINI,R.BERNI REMARK 1 TITL IDENTIFICATION, RETINOID BINDING AND X-RAY ANALYSIS OF A REMARK 1 TITL 2 HUMAN RETINOL-BINDING PROTEIN REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 98 3710 2001 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.061455898 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.44 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) (%) : 87.8 REMARK 3 NUMBER OF REFLECTIONS : 7579 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) : 0.230 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.700 REMARK 3 FREE R VALUE TEST SET COUNT : 809 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1126 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 132 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1084 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.32000 REMARK 3 B22 (A**2) : 5.57000 REMARK 3 B33 (A**2) : -1.25000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.88000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL 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) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 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) : 27.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 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) : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.42 REMARK 3 BSOL : 112.5 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.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LPJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-02. REMARK 100 THE DEPOSITION ID IS D_1000016161. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7611 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 28.606 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : 0.12400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.38200 REMARK 200 R SYM FOR SHELL (I) : 0.12400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 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: 1CRB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 4000, 10% ISOPROPANOL, 100 MM REMARK 280 SODIUM CITRATE, PH 5.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 17.02650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.59300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 17.02650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.59300 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 148 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 251 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 288 LIES ON A SPECIAL POSITION. 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 ARG A 58 146.82 -176.10 REMARK 500 ASN A 74 39.65 -94.42 REMARK 500 ARG A 75 6.36 -68.30 REMARK 500 LEU A 77 -101.76 -126.81 REMARK 500 ASN A 90 -96.84 56.30 REMARK 500 CYS A 121 119.12 -160.25 REMARK 500 GLU A 122 64.95 24.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CRB RELATED DB: PDB REMARK 900 CELLULAR RETINOL BINDING PROTEIN (CRBP) COMPLEXED WITH ALL-TRANS REMARK 900 RETINOL REMARK 900 RELATED ID: 1OPA RELATED DB: PDB REMARK 900 CELLULAR RETINOL BINDING PROTEIN II (APO FORM) (APO-CRBPII) REMARK 900 RELATED ID: 1OPB RELATED DB: PDB REMARK 900 CELLULAR RETINOL BINDING PROTEIN II (HOLO FORM) (HOLO-CRBPII) REMARK 900 RELATED ID: 1GGL RELATED DB: PDB REMARK 900 HUMAN CELLULAR RETINOL BINDING PROTEIN III DBREF 1LPJ A 1 133 UNP Q96R05 RET7_HUMAN 2 134 SEQRES 1 A 133 PRO ALA ASP LEU SER GLY THR TRP THR LEU LEU SER SER SEQRES 2 A 133 ASP ASN PHE GLU GLY TYR MET LEU ALA LEU GLY ILE ASP SEQRES 3 A 133 PHE ALA THR ARG LYS ILE ALA LYS LEU LEU LYS PRO GLN SEQRES 4 A 133 LYS VAL ILE GLU GLN ASN GLY ASP SER PHE THR ILE HIS SEQRES 5 A 133 THR ASN SER SER LEU ARG ASN TYR PHE VAL LYS PHE LYS SEQRES 6 A 133 VAL GLY GLU GLU PHE ASP GLU ASP ASN ARG GLY LEU ASP SEQRES 7 A 133 ASN ARG LYS CYS LYS SER LEU VAL ILE TRP ASP ASN ASP SEQRES 8 A 133 ARG LEU THR CYS ILE GLN LYS GLY GLU LYS LYS ASN ARG SEQRES 9 A 133 GLY TRP THR HIS TRP ILE GLU GLY ASP LYS LEU HIS LEU SEQRES 10 A 133 GLU MET PHE CYS GLU GLY GLN VAL CYS LYS GLN THR PHE SEQRES 11 A 133 GLN ARG ALA FORMUL 2 HOH *150(H2 O) HELIX 1 1 ASN A 15 GLY A 24 1 10 HELIX 2 2 ASP A 26 LYS A 34 1 9 SHEET 1 A10 TYR A 60 LYS A 65 0 SHEET 2 A10 SER A 48 ASN A 54 -1 N THR A 53 O TYR A 60 SHEET 3 A10 GLN A 39 ASN A 45 -1 N VAL A 41 O HIS A 52 SHEET 4 A10 GLY A 6 ASP A 14 -1 N TRP A 8 O LYS A 40 SHEET 5 A10 GLN A 124 ARG A 132 -1 O GLN A 131 N THR A 9 SHEET 6 A10 LYS A 114 CYS A 121 -1 N MET A 119 O CYS A 126 SHEET 7 A10 ARG A 104 GLU A 111 -1 N TRP A 109 O HIS A 116 SHEET 8 A10 ARG A 92 GLY A 99 -1 N CYS A 95 O TRP A 106 SHEET 9 A10 LYS A 81 ASP A 89 -1 N ASP A 89 O ARG A 92 SHEET 10 A10 PHE A 70 ASP A 73 -1 N GLU A 72 O CYS A 82 CRYST1 34.053 57.186 67.939 90.00 104.03 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 0.029366 0.000000 0.007338 0.00000 SCALE2 0.000000 0.017487 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015172 0.00000