HEADER CELLULAR LIPOPHILIC TRANSPORT PROTEIN 10-FEB-93 1CRB TITLE CRYSTALLOGRAPHIC STUDIES ON A FAMILY OF CELLULAR LIPOPHILIC TRANSPORT TITLE 2 PROTEINS. REFINEMENT OF P2 MYELIN PROTEIN AND THE STRUCTURE TITLE 3 DETERMINATION AND REFINEMENT OF CELLULAR RETINOL-BINDING PROTEIN IN TITLE 4 COMPLEX WITH ALL-TRANS-RETINOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR RETINOL BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS RATTUS; SOURCE 3 ORGANISM_COMMON: BLACK RAT; SOURCE 4 ORGANISM_TAXID: 10117 KEYWDS CELLULAR LIPOPHILIC TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.W.COWAN,T.A.JONES REVDAT 4 07-FEB-24 1CRB 1 REMARK LINK REVDAT 3 29-NOV-17 1CRB 1 HELIX REVDAT 2 24-FEB-09 1CRB 1 VERSN REVDAT 1 20-DEC-94 1CRB 0 JRNL AUTH S.W.COWAN,M.E.NEWCOMER,T.A.JONES JRNL TITL CRYSTALLOGRAPHIC STUDIES ON A FAMILY OF CELLULAR LIPOPHILIC JRNL TITL 2 TRANSPORT PROTEINS. REFINEMENT OF P2 MYELIN PROTEIN AND THE JRNL TITL 3 STRUCTURE DETERMINATION AND REFINEMENT OF CELLULAR JRNL TITL 4 RETINOL-BINDING PROTEIN IN COMPLEX WITH ALL-TRANS-RETINOL. JRNL REF J.MOL.BIOL. V. 230 1225 1993 JRNL REFN ISSN 0022-2836 JRNL PMID 7683727 JRNL DOI 10.1006/JMBI.1993.1238 REMARK 1 REMARK 1 REFERENCE 1 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 REFERENCE 2 REMARK 1 AUTH M.C.ZAPPONI,G.ZANOTTI,M.STOPPINI,R.BERNI REMARK 1 TITL THE PRIMARY STRUCTURE OF PISCINE (ONCORHYNCHUS MYKISS) REMARK 1 TITL 2 RETINOL-BINDING PROTEIN AND A COMPARISON WITH THE REMARK 1 TITL 3 THREE-DIMENSIONAL STRUCTURE OF MAMMALIAN RETINOL-BINDING REMARK 1 TITL 4 PROTEIN REMARK 1 REF EUR.J.BIOCHEM. V. 210 937 1992 REMARK 1 REFN ISSN 0014-2956 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.W.COWAN,M.E.NEWCOMER,T.A.JONES REMARK 1 TITL CRYSTALLOGRAPHIC REFINEMENT OF HUMAN SERUM RETINOL BINDING REMARK 1 TITL 2 PROTEIN AT 2 ANGSTROMS RESOLUTION REMARK 1 REF PROTEINS V. 8 44 1990 REMARK 1 REFN ISSN 0887-3585 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.E.NEWCOMER,A.LILJAS,V.ERIKSSON,J.SUNDELIN,L.RASK, REMARK 1 AUTH 2 P.A.PETERSON REMARK 1 TITL CRYSTALLIZATION OF AND PRELIMINARY X-RAY DATA FOR AN REMARK 1 TITL 2 INTRACELLULAR VITAMIN A-BINDING PROTEIN FROM RAT LIVER REMARK 1 REF J.BIOL.CHEM. V. 256 8162 1981 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL 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) : 0.188 REMARK 3 FREE R VALUE : 0.248 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 : 1102 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 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) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.310 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.990 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 1CRB 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_1000172474. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 20.04500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.67000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.69500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.67000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.04500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.69500 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 ASP A 24 30.15 70.51 REMARK 500 LYS A 37 77.94 -117.16 REMARK 500 LEU A 74 34.21 -87.60 REMARK 500 ILE A 77 -75.42 -100.83 REMARK 500 ALA A 121 128.84 -174.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 201 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 18 OE1 REMARK 620 2 GLU A 18 OE2 49.5 REMARK 620 3 ASP A 91 OD2 99.8 100.8 REMARK 620 4 ASP A 91 OD1 132.6 94.9 51.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 202 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 102 OE2 REMARK 620 2 GLU A 102 OE1 46.8 REMARK 620 3 GLU A 118 OE1 97.6 94.4 REMARK 620 4 GLU A 118 OE2 116.8 80.0 48.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RTL A 200 DBREF 1CRB A 1 134 UNP P02696 RET1_RAT 1 134 SEQRES 1 A 134 PRO VAL ASP PHE ASN GLY TYR TRP LYS MET LEU SER ASN SEQRES 2 A 134 GLU ASN PHE GLU GLU TYR LEU ARG ALA LEU ASP VAL ASN SEQRES 3 A 134 VAL ALA LEU ARG LYS ILE ALA ASN LEU LEU LYS PRO ASP SEQRES 4 A 134 LYS GLU ILE VAL GLN ASP GLY ASP HIS MET ILE ILE ARG SEQRES 5 A 134 THR LEU SER THR PHE ARG ASN TYR ILE MET ASP PHE GLN SEQRES 6 A 134 VAL GLY LYS GLU PHE GLU GLU ASP LEU THR GLY ILE ASP SEQRES 7 A 134 ASP ARG LYS CYS MET THR THR VAL SER TRP ASP GLY ASP SEQRES 8 A 134 LYS LEU GLN CYS VAL GLN LYS GLY GLU LYS GLU GLY ARG SEQRES 9 A 134 GLY TRP THR GLN TRP ILE GLU GLY ASP GLU LEU HIS LEU SEQRES 10 A 134 GLU MET ARG ALA GLU GLY VAL THR CYS LYS GLN VAL PHE SEQRES 11 A 134 LYS LYS VAL HIS HET CD A 201 1 HET CD A 202 1 HET RTL A 200 21 HETNAM CD CADMIUM ION HETNAM RTL RETINOL FORMUL 2 CD 2(CD 2+) FORMUL 4 RTL C20 H30 O FORMUL 5 HOH *73(H2 O) HELIX 1 H1 VAL A 2 ASN A 5 53/10 HELIX 4 HELIX 2 A PHE A 16 LEU A 23 1ALPHA A 8 HELIX 3 B VAL A 27 LEU A 35 1ALPHA B 9 SHEET 1 SA11 GLY A 6 GLU A 14 0 SHEET 2 SA11 LYS A 37 ASP A 45 -1 SHEET 3 SA11 HIS A 48 SER A 55 -1 SHEET 4 SA11 ASN A 59 GLN A 65 -1 SHEET 5 SA11 GLU A 69 LEU A 74 -1 SHEET 6 SA11 ARG A 80 ASP A 89 -1 SHEET 7 SA11 LYS A 92 GLY A 99 -1 SHEET 8 SA11 ARG A 104 GLU A 111 -1 SHEET 9 SA11 GLU A 114 ALA A 121 -1 SHEET 10 SA11 VAL A 124 LYS A 132 -1 SHEET 11 SA11 GLY A 6 GLU A 14 -1 LINK OE1 GLU A 18 CD CD A 201 4445 1555 2.64 LINK OE2 GLU A 18 CD CD A 201 4445 1555 2.62 LINK OD2 ASP A 91 CD CD A 201 1555 1555 2.62 LINK OD1 ASP A 91 CD CD A 201 1555 1555 2.47 LINK OE2 GLU A 102 CD CD A 202 4445 1555 2.79 LINK OE1 GLU A 102 CD CD A 202 4445 1555 2.76 LINK OE1 GLU A 118 CD CD A 202 1555 1555 2.59 LINK OE2 GLU A 118 CD CD A 202 1555 1555 2.79 SITE 1 AC1 2 GLU A 18 ASP A 91 SITE 1 AC2 2 GLU A 102 GLU A 118 SITE 1 AC3 7 ALA A 33 LYS A 40 ILE A 51 THR A 53 SITE 2 AC3 7 ARG A 58 TRP A 106 GLN A 108 CRYST1 40.090 47.390 69.340 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 0.024944 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021101 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014422 0.00000