HEADER TRANSPORT PROTEIN 08-JAN-02 1KQX TITLE CRYSTAL STRUCTURE OF APO-CRBP FROM ZEBRAFISH COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR RETINOL-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CRBP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RETINOL, VITAMIN A, RETINOL-BINDING, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.CALDERONE,C.FOLLI,A.MARCHESANI,R.BERNI,G.ZANOTTI REVDAT 4 03-APR-24 1KQX 1 REMARK REVDAT 3 14-FEB-24 1KQX 1 REMARK REVDAT 2 24-FEB-09 1KQX 1 VERSN REVDAT 1 28-AUG-02 1KQX 0 JRNL AUTH V.CALDERONE,C.FOLLI,A.MARCHESANI,R.BERNI,G.ZANOTTI JRNL TITL IDENTIFICATION AND STRUCTURAL ANALYSIS OF A ZEBRAFISH APO JRNL TITL 2 AND HOLO CELLULAR RETINOL-BINDING PROTEIN. JRNL REF J.MOL.BIOL. V. 321 527 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12162964 JRNL DOI 10.1016/S0022-2836(02)00628-9 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. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.203 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.195 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 805 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 16211 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.194 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.188 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 701 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 13158 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1103 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1237.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4963 REMARK 3 NUMBER OF RESTRAINTS : 4485 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.034 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.049 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.034 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.088 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KQX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015248. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-01 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 : ID14-4 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 : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16380 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : 4.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.29400 REMARK 200 R SYM FOR SHELL (I) : 0.29400 REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: HOLO RAT CRBPII REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, AMMONIUM ACETATE, SODIUM REMARK 280 CITRATE, PH 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 44.37950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.37950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.21850 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 44.37950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.37950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.21850 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 44.37950 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 44.37950 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 19.21850 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 44.37950 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 44.37950 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 19.21850 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 30 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG A 30 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 30 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 104 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 PHE A 57 -87.55 -74.50 REMARK 500 LEU A 77 -94.76 -130.77 REMARK 500 GLN A 122 -125.97 54.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CRB RELATED DB: PDB REMARK 900 RAT CRBPI REMARK 900 RELATED ID: 1OPB RELATED DB: PDB REMARK 900 RAT HOLO-CRBPII REMARK 900 RELATED ID: 1OPA RELATED DB: PDB REMARK 900 RAT APO-CRBPII REMARK 900 RELATED ID: 1KQW RELATED DB: PDB REMARK 900 HOLO-CRBP FROM ZEBRAFISH DBREF 1KQX A 1 134 UNP Q8UVG6 Q8UVG6_BRARE 2 135 SEQRES 1 A 134 PRO ALA ASP PHE ASN GLY THR TRP GLU MET LEU SER ASN SEQRES 2 A 134 ASP ASN PHE GLU ASP VAL MET LYS ALA LEU ASP ILE ASP SEQRES 3 A 134 PHE ALA THR ARG LYS ILE ALA VAL HIS LEU LYS GLN THR SEQRES 4 A 134 LYS VAL ILE VAL GLN ASN GLY ASP LYS PHE GLU THR LYS SEQRES 5 A 134 THR LEU SER THR PHE ARG ASN TYR GLU VAL ASN PHE VAL SEQRES 6 A 134 ILE GLY GLU GLU PHE ASP GLU GLN THR LYS GLY LEU ASP SEQRES 7 A 134 ASN ARG THR VAL LYS THR LEU VAL LYS TRP ASP GLY ASP SEQRES 8 A 134 LYS LEU VAL CYS VAL GLN LYS GLY GLU LYS GLU ASN ARG SEQRES 9 A 134 GLY TRP LYS GLN TRP ILE GLU GLY ASP LEU LEU HIS LEU SEQRES 10 A 134 GLU ILE HIS CYS GLN ASP LYS VAL CYS HIS GLN VAL PHE SEQRES 11 A 134 LYS LYS LYS ASN FORMUL 2 HOH *126(H2 O) HELIX 1 1 ASN A 15 LEU A 23 1 9 HELIX 2 2 ASP A 26 VAL A 34 1 9 SHEET 1 A10 TYR A 60 VAL A 65 0 SHEET 2 A10 LYS A 48 SER A 55 -1 N THR A 53 O TYR A 60 SHEET 3 A10 GLN A 38 ASN A 45 -1 N VAL A 41 O LYS A 52 SHEET 4 A10 GLY A 6 ASP A 14 -1 N TRP A 8 O LYS A 40 SHEET 5 A10 LYS A 124 LYS A 132 -1 O LYS A 131 N GLU A 9 SHEET 6 A10 LEU A 114 CYS A 121 -1 N ILE A 119 O CYS A 126 SHEET 7 A10 GLY A 105 GLU A 111 -1 N TRP A 109 O HIS A 116 SHEET 8 A10 LYS A 92 LYS A 98 -1 N CYS A 95 O TRP A 106 SHEET 9 A10 THR A 81 ASP A 89 -1 N LYS A 83 O LYS A 98 SHEET 10 A10 PHE A 70 GLN A 73 -1 N GLU A 72 O VAL A 82 CRYST1 88.759 88.759 38.437 90.00 90.00 90.00 I 4 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 0.011266 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011266 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026017 0.00000