HEADER RETINOL-BINDING PROTEIN 18-JUL-16 5LJC TITLE CRYSTAL STRUCTURE OF HOLO HUMAN CRBP1 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; COMPND 7 OTHER_DETAILS: POSITION 108 WAS MUTATED IN LEU. Q108L 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS RETINOL, VITAMIN A, RETINOL-BINDING PROTEIN, RBP EXPDTA X-RAY DIFFRACTION AUTHOR G.ZANOTTI,F.VALLESE,R.BERNI,I.MENOZZI REVDAT 3 10-JAN-24 5LJC 1 REMARK REVDAT 2 29-MAR-17 5LJC 1 JRNL REVDAT 1 18-JAN-17 5LJC 0 JRNL AUTH I.MENOZZI,F.VALLESE,E.POLVERINI,C.FOLLI,R.BERNI,G.ZANOTTI JRNL TITL STRUCTURAL AND MOLECULAR DETERMINANTS AFFECTING THE JRNL TITL 2 INTERACTION OF RETINOL WITH HUMAN CRBP1. JRNL REF J. STRUCT. BIOL. V. 197 330 2017 JRNL REFN ESSN 1095-8657 JRNL PMID 28057518 JRNL DOI 10.1016/J.JSB.2016.12.012 REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.250 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 23559 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2183 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 40.8992 - 3.6091 0.99 2642 132 0.1420 0.1680 REMARK 3 2 3.6091 - 2.8649 0.99 2601 142 0.1547 0.1795 REMARK 3 3 2.8649 - 2.5028 0.99 2625 140 0.1771 0.1966 REMARK 3 4 2.5028 - 2.2740 0.98 2580 134 0.1782 0.2064 REMARK 3 5 2.2740 - 2.1110 0.98 2622 131 0.1797 0.2567 REMARK 3 6 2.1110 - 1.9865 0.99 2614 135 0.1804 0.2345 REMARK 3 7 1.9865 - 1.8871 0.99 2603 140 0.2056 0.2684 REMARK 3 8 1.8871 - 1.8049 0.99 2616 138 0.2124 0.2176 REMARK 3 9 1.8049 - 1.7354 0.99 2654 139 0.2127 0.2607 REMARK 3 10 1.7354 - 1.6755 0.99 2624 140 0.1997 0.2180 REMARK 3 11 1.6755 - 1.6231 0.99 2643 136 0.2153 0.2710 REMARK 3 12 1.6231 - 1.5767 0.99 2611 139 0.2301 0.2675 REMARK 3 13 1.5767 - 1.5352 0.99 2648 139 0.2332 0.2756 REMARK 3 14 1.5352 - 1.4978 0.99 2622 140 0.2657 0.2856 REMARK 3 15 1.4978 - 1.4637 0.98 2588 131 0.2686 0.3011 REMARK 3 16 1.4637 - 1.4326 0.88 2310 127 0.3020 0.3259 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.130 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 : 0.012 1183 REMARK 3 ANGLE : 1.713 1591 REMARK 3 CHIRALITY : 0.074 167 REMARK 3 PLANARITY : 0.007 198 REMARK 3 DIHEDRAL : 14.831 469 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 5LJC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1200000830. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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) : 0.91881 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23562 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 40.883 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.50400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5LJB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CHLORIDE, 0.1 M SODIUM REMARK 280 ACETATE, 0.2 MM ZINC CHLORIDE, PH 5,0, 20% PEG 6000, PH 5.0, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 279K 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 17.01750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.87400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.28150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.87400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.01750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.28150 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HZ1 LYS A 68 O HOH A 308 1.56 REMARK 500 O HOH A 303 O HOH A 350 1.92 REMARK 500 OH TYR A 7 O HOH A 301 1.92 REMARK 500 OE1 GLU A 18 O HOH A 302 1.97 REMARK 500 OD2 ASP A 63 O HOH A 303 2.02 REMARK 500 O HOH A 374 O HOH A 442 2.08 REMARK 500 O LEU A 35 O HOH A 304 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 303 O HOH A 328 4455 2.01 REMARK 500 O HOH A 328 O HOH A 350 4555 2.03 REMARK 500 O HOH A 303 O HOH A 372 1455 2.08 REMARK 500 O HOH A 375 O HOH A 399 3544 2.19 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 LEU A 74 32.28 -92.94 REMARK 500 ILE A 77 -86.21 -104.17 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 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 427 O REMARK 620 2 HOH A 437 O 127.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RTL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5LJB RELATED DB: PDB DBREF 5LJC A 0 134 UNP P09455 RET1_HUMAN 1 135 SEQADV 5LJC LEU A 108 UNP P09455 GLN 109 ENGINEERED MUTATION SEQRES 1 A 135 MET PRO VAL ASP PHE THR GLY TYR TRP LYS MET LEU VAL SEQRES 2 A 135 ASN GLU ASN PHE GLU GLU TYR LEU ARG ALA LEU ASP VAL SEQRES 3 A 135 ASN VAL ALA LEU ARG LYS ILE ALA ASN LEU LEU LYS PRO SEQRES 4 A 135 ASP LYS GLU ILE VAL GLN ASP GLY ASP HIS MET ILE ILE SEQRES 5 A 135 ARG THR LEU SER THR PHE ARG ASN TYR ILE MET ASP PHE SEQRES 6 A 135 GLN VAL GLY LYS GLU PHE GLU GLU ASP LEU THR GLY ILE SEQRES 7 A 135 ASP ASP ARG LYS CYS MET THR THR VAL SER TRP ASP GLY SEQRES 8 A 135 ASP LYS LEU GLN CYS VAL GLN LYS GLY GLU LYS GLU GLY SEQRES 9 A 135 ARG GLY TRP THR LEU TRP ILE GLU GLY ASP GLU LEU HIS SEQRES 10 A 135 LEU GLU MET ARG VAL GLU GLY VAL VAL CYS LYS GLN VAL SEQRES 11 A 135 PHE LYS LYS VAL GLN HET RTL A 201 102 HET NA A 202 1 HETNAM RTL RETINOL HETNAM NA SODIUM ION FORMUL 2 RTL C20 H30 O FORMUL 3 NA NA 1+ FORMUL 4 HOH *178(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 TRP A 8 O LYS A 40 SHEET 5 AA110 VAL A 124 LYS A 131 -1 O LYS A 127 N GLU A 14 SHEET 6 AA110 GLU A 114 VAL A 121 -1 N LEU A 117 O GLN A 128 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 CYS A 95 O TRP A 106 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 PHE A 70 O THR A 84 LINK NA NA A 202 O HOH A 427 1555 1555 2.87 LINK NA NA A 202 O HOH A 437 1555 1555 3.19 SITE 1 AC1 12 LEU A 20 LYS A 40 ILE A 51 THR A 53 SITE 2 AC1 12 PHE A 57 ARG A 58 MET A 62 GLY A 76 SITE 3 AC1 12 ILE A 77 TRP A 106 MET A 119 HOH A 309 SITE 1 AC2 4 LYS A 37 SER A 55 THR A 56 HOH A 427 CRYST1 34.035 48.563 75.748 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 0.029382 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020592 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013202 0.00000