HEADER RETINOL-BINDING PROTEIN 29-DEC-15 5HA1 TITLE CRYSTAL STRUCTURE OF HUMAN CELLULAR RETINOL BINDING PROTEIN 1 IN TITLE 2 COMPLEX WITH RETINYLAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOL-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELLULAR RETINOL-BINDING PROTEIN,CRBP,CELLULAR RETINOL- COMPND 5 BINDING PROTEIN I,CRBP-I; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RBP1, CRBP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS RETINYLAMINE, RETINOL, BINDING PROTEIN, RETINOL-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.GOLCZAK,J.M.ARNE,J.A.SILVAROLI,P.D.KISER,S.BANERJEE REVDAT 6 27-SEP-23 5HA1 1 REMARK REVDAT 5 11-DEC-19 5HA1 1 REMARK REVDAT 4 13-SEP-17 5HA1 1 JRNL REMARK REVDAT 3 11-MAY-16 5HA1 1 JRNL REVDAT 2 23-MAR-16 5HA1 1 JRNL REVDAT 1 02-MAR-16 5HA1 0 JRNL AUTH J.A.SILVAROLI,J.M.ARNE,S.CHELSTOWSKA,P.D.KISER,S.BANERJEE, JRNL AUTH 2 M.GOLCZAK JRNL TITL LIGAND BINDING INDUCES CONFORMATIONAL CHANGES IN HUMAN JRNL TITL 2 CELLULAR RETINOL-BINDING PROTEIN 1 (CRBP1) REVEALED BY JRNL TITL 3 ATOMIC RESOLUTION CRYSTAL STRUCTURES. JRNL REF J.BIOL.CHEM. V. 291 8528 2016 JRNL REFN ESSN 1083-351X JRNL PMID 26900151 JRNL DOI 10.1074/JBC.M116.714535 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10PRE_2138 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 30442 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.124 REMARK 3 R VALUE (WORKING SET) : 0.122 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1548 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 3.0014 - 2.3827 1.00 2667 140 0.1311 0.1564 REMARK 3 2 2.3827 - 2.0816 1.00 2640 139 0.1066 0.1482 REMARK 3 3 2.0816 - 1.8914 1.00 2632 139 0.0970 0.1204 REMARK 3 4 1.8914 - 1.7558 1.00 2594 154 0.1009 0.1428 REMARK 3 5 1.7558 - 1.6523 1.00 2615 131 0.0983 0.1471 REMARK 3 6 1.6523 - 1.5696 1.00 2608 137 0.1074 0.1519 REMARK 3 7 1.5696 - 1.5013 1.00 2562 147 0.1128 0.1849 REMARK 3 8 1.5013 - 1.4435 1.00 2596 146 0.1205 0.1623 REMARK 3 9 1.4435 - 1.3937 1.00 2577 130 0.1358 0.2107 REMARK 3 10 1.3937 - 1.3501 1.00 2594 132 0.1543 0.2184 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 1250 REMARK 3 ANGLE : 1.131 1690 REMARK 3 CHIRALITY : 0.087 174 REMARK 3 PLANARITY : 0.007 219 REMARK 3 DIHEDRAL : 18.820 480 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5HA1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216728. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30442 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 27.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.01030 REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.60400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1CRB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, 25% PEG 6000, PH 5.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 18.57500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.65000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.78500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.65000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.57500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.78500 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 68 CG CD CE NZ 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 52 NE - CZ - NH1 ANGL. DEV. = 3.6 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 ILE A 77 -88.96 -102.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 580 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 581 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 582 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 583 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 584 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A 585 DISTANCE = 6.22 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RNE A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5H8T RELATED DB: PDB REMARK 900 RELATED ID: 5H9A RELATED DB: PDB REMARK 900 RELATED ID: 5HBS RELATED DB: PDB DBREF 5HA1 A 1 134 UNP P09455 RET1_HUMAN 2 135 SEQADV 5HA1 HIS A 135 UNP P09455 EXPRESSION TAG SEQADV 5HA1 HIS A 136 UNP P09455 EXPRESSION TAG SEQADV 5HA1 HIS A 137 UNP P09455 EXPRESSION TAG SEQADV 5HA1 HIS A 138 UNP P09455 EXPRESSION TAG SEQADV 5HA1 HIS A 139 UNP P09455 EXPRESSION TAG SEQADV 5HA1 HIS A 140 UNP P09455 EXPRESSION TAG SEQRES 1 A 140 PRO VAL ASP PHE THR GLY TYR TRP LYS MET LEU VAL ASN SEQRES 2 A 140 GLU ASN PHE GLU GLU TYR LEU ARG ALA LEU ASP VAL ASN SEQRES 3 A 140 VAL ALA LEU ARG LYS ILE ALA ASN LEU LEU LYS PRO ASP SEQRES 4 A 140 LYS GLU ILE VAL GLN ASP GLY ASP HIS MET ILE ILE ARG SEQRES 5 A 140 THR LEU SER THR PHE ARG ASN TYR ILE MET ASP PHE GLN SEQRES 6 A 140 VAL GLY LYS GLU PHE GLU GLU ASP LEU THR GLY ILE ASP SEQRES 7 A 140 ASP ARG LYS CYS MET THR THR VAL SER TRP ASP GLY ASP SEQRES 8 A 140 LYS LEU GLN CYS VAL GLN LYS GLY GLU LYS GLU GLY ARG SEQRES 9 A 140 GLY TRP THR GLN TRP ILE GLU GLY ASP GLU LEU HIS LEU SEQRES 10 A 140 GLU MET ARG VAL GLU GLY VAL VAL CYS LYS GLN VAL PHE SEQRES 11 A 140 LYS LYS VAL GLN HIS HIS HIS HIS HIS HIS HET RNE A 201 52 HETNAM RNE (2~{E},4~{E},6~{E},8~{E})-3,7-DIMETHYL-9-(2,6,6- HETNAM 2 RNE TRIMETHYLCYCLOHEXEN-1-YL)NONA-2,4,6,8-TETRAEN-1-AMINE FORMUL 2 RNE C20 H31 N FORMUL 3 HOH *285(H2 O) HELIX 1 AA1 ASN A 15 LEU A 23 1 9 HELIX 2 AA2 ASN A 26 ASN A 34 1 9 SHEET 1 AA110 TYR A 60 GLN A 65 0 SHEET 2 AA110 HIS A 48 LEU A 54 -1 N THR A 53 O TYR A 60 SHEET 3 AA110 ASP A 39 ASP A 45 -1 N GLU A 41 O ARG A 52 SHEET 4 AA110 GLY A 6 GLU A 14 -1 N GLY A 6 O ILE A 42 SHEET 5 AA110 VAL A 124 VAL A 133 -1 O LYS A 127 N GLU A 14 SHEET 6 AA110 GLU A 114 VAL A 121 -1 N MET A 119 O CYS A 126 SHEET 7 AA110 GLY A 105 GLU A 111 -1 N TRP A 109 O HIS A 116 SHEET 8 AA110 LYS A 92 LYS A 98 -1 N LEU A 93 O GLN A 108 SHEET 9 AA110 LYS A 81 ASP A 89 -1 N SER A 87 O GLN A 94 SHEET 10 AA110 PHE A 70 ASP A 73 -1 N GLU A 72 O CYS A 82 SITE 1 AC1 10 LEU A 20 LEU A 29 LYS A 40 ILE A 51 SITE 2 AC1 10 GLY A 76 ILE A 77 TRP A 106 GLN A 108 SITE 3 AC1 10 LEU A 117 MET A 119 CRYST1 37.150 49.570 73.300 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 0.026918 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020173 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013643 0.00000