HEADER LIPID BINDING PROTEIN 11-OCT-18 6MQX TITLE CRYSTAL STRUCTURE OF ALL-TRANS RETINAL-BOUND TITLE 2 R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121E HUMAN CELLULAR RETINOIC ACID TITLE 3 BINDING PROTEIN II IRRADIATED WITH 400 NM LASER (30 SECONDS) AND TITLE 4 SUBSEQUENTLY DARK ADAPTED (25 MINUTES) AT 2.0 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR RETINOIC ACID-BINDING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: R111K, Y134F, T54V, R132Q, P39Y, R59Y, L121E; COMPND 5 SYNONYM: CELLULAR RETINOIC ACID-BINDING PROTEIN II,CRABP-II; 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: CRABP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS ILBP, RHODOPSIN MIMIC, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.GHANBARPOUR,J.GEIGER REVDAT 4 11-OCT-23 6MQX 1 REMARK REVDAT 3 18-DEC-19 6MQX 1 REMARK REVDAT 2 13-FEB-19 6MQX 1 JRNL REVDAT 1 09-JAN-19 6MQX 0 JRNL AUTH A.GHANBARPOUR,M.NAIRAT,M.NOSRATI,E.M.SANTOS,C.VASILEIOU, JRNL AUTH 2 M.DANTUS,B.BORHAN,J.H.GEIGER JRNL TITL MIMICKING MICROBIAL RHODOPSIN ISOMERIZATION IN A SINGLE JRNL TITL 2 CRYSTAL. JRNL REF J. AM. CHEM. SOC. V. 141 1735 2019 JRNL REFN ESSN 1520-5126 JRNL PMID 30580520 JRNL DOI 10.1021/JACS.8B12493 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260) 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 13658 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1364 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 35.5899 - 4.3281 0.99 1314 149 0.1751 0.1931 REMARK 3 2 4.3281 - 3.4363 1.00 1255 137 0.1763 0.2246 REMARK 3 3 3.4363 - 3.0022 0.99 1254 133 0.2105 0.2655 REMARK 3 4 3.0022 - 2.7278 1.00 1222 137 0.2438 0.2620 REMARK 3 5 2.7278 - 2.5323 1.00 1201 134 0.2510 0.2911 REMARK 3 6 2.5323 - 2.3830 1.00 1219 139 0.2318 0.3035 REMARK 3 7 2.3830 - 2.2637 1.00 1200 134 0.2305 0.2616 REMARK 3 8 2.2637 - 2.1652 0.99 1202 134 0.2142 0.2391 REMARK 3 9 2.1652 - 2.0819 1.00 1217 135 0.2263 0.2800 REMARK 3 10 2.0819 - 2.0100 1.00 1210 132 0.2380 0.2566 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.760 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 : 0.007 1183 REMARK 3 ANGLE : 0.863 1606 REMARK 3 CHIRALITY : 0.055 183 REMARK 3 PLANARITY : 0.004 205 REMARK 3 DIHEDRAL : 8.916 982 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 6MQX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000236943. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97911 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13679 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 35.584 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 44.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.60 REMARK 200 R MERGE FOR SHELL (I) : 0.62000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 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: 4YFP REMARK 200 REMARK 200 REMARK: HEXAGONAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, DL-MALIC ACID, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.32733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 66.65467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 66.65467 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.32733 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 -87.75150 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 -50.66335 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 33.32733 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 ASN A 115 CG OD1 ND2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 127 CG 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 THR A 56 -163.42 -123.12 REMARK 500 THR A 56 -167.63 -118.77 REMARK 500 GLU A 73 -146.95 -137.20 REMARK 500 SER A 89 -168.14 -169.72 REMARK 500 ASP A 126 -112.39 52.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RET A 203 DBREF 6MQX A 1 137 UNP P29373 RABP2_HUMAN 2 138 SEQADV 6MQX TYR A 39 UNP P29373 PRO 40 ENGINEERED MUTATION SEQADV 6MQX VAL A 54 UNP P29373 THR 55 ENGINEERED MUTATION SEQADV 6MQX TYR A 59 UNP P29373 ARG 60 ENGINEERED MUTATION SEQADV 6MQX LYS A 111 UNP P29373 ARG 112 ENGINEERED MUTATION SEQADV 6MQX GLU A 121 UNP P29373 LEU 122 ENGINEERED MUTATION SEQADV 6MQX GLN A 132 UNP P29373 ARG 133 ENGINEERED MUTATION SEQADV 6MQX PHE A 134 UNP P29373 TYR 135 ENGINEERED MUTATION SEQRES 1 A 137 PRO ASN PHE SER GLY ASN TRP LYS ILE ILE ARG SER GLU SEQRES 2 A 137 ASN PHE GLU GLU LEU LEU LYS VAL LEU GLY VAL ASN VAL SEQRES 3 A 137 MET LEU ARG LYS ILE ALA VAL ALA ALA ALA SER LYS TYR SEQRES 4 A 137 ALA VAL GLU ILE LYS GLN GLU GLY ASP THR PHE TYR ILE SEQRES 5 A 137 LYS VAL SER THR THR VAL TYR THR THR GLU ILE ASN PHE SEQRES 6 A 137 LYS VAL GLY GLU GLU PHE GLU GLU GLN THR VAL ASP GLY SEQRES 7 A 137 ARG PRO CYS LYS SER LEU VAL LYS TRP GLU SER GLU ASN SEQRES 8 A 137 LYS MET VAL CYS GLU GLN LYS LEU LEU LYS GLY GLU GLY SEQRES 9 A 137 PRO LYS THR SER TRP THR LYS GLU LEU THR ASN ASP GLY SEQRES 10 A 137 GLU LEU ILE GLU THR MET THR ALA ASP ASP VAL VAL CYS SEQRES 11 A 137 THR GLN VAL PHE VAL ARG GLU HET GOL A 201 6 HET GOL A 202 6 HET RET A 203 20 HETNAM GOL GLYCEROL HETNAM RET RETINAL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 RET C20 H28 O FORMUL 5 HOH *38(H2 O) HELIX 1 AA1 ASN A 14 LEU A 22 1 9 HELIX 2 AA2 ASN A 25 SER A 37 1 13 SHEET 1 AA110 THR A 60 LYS A 66 0 SHEET 2 AA110 THR A 49 SER A 55 -1 N ILE A 52 O ILE A 63 SHEET 3 AA110 ALA A 40 GLU A 46 -1 N GLU A 42 O LYS A 53 SHEET 4 AA110 GLY A 5 GLU A 13 -1 N TRP A 7 O VAL A 41 SHEET 5 AA110 VAL A 128 ARG A 136 -1 O VAL A 135 N LYS A 8 SHEET 6 AA110 LEU A 119 ALA A 125 -1 N MET A 123 O CYS A 130 SHEET 7 AA110 THR A 107 LEU A 113 -1 N GLU A 112 O ILE A 120 SHEET 8 AA110 LYS A 92 LEU A 99 -1 N CYS A 95 O TRP A 109 SHEET 9 AA110 PRO A 80 SER A 89 -1 N GLU A 88 O LYS A 92 SHEET 10 AA110 PHE A 71 GLN A 74 -1 N PHE A 71 O SER A 83 LINK NZ LYS A 111 C15 RET A 203 1555 1555 1.26 SITE 1 AC1 2 ASN A 64 GLU A 69 SITE 1 AC2 4 GLU A 62 ASN A 64 GLU A 72 GLU A 73 SITE 1 AC3 10 MET A 27 ILE A 31 TYR A 39 ILE A 52 SITE 2 AC3 10 THR A 56 ILE A 63 VAL A 76 TRP A 109 SITE 3 AC3 10 LYS A 111 GLU A 121 CRYST1 58.501 58.501 99.982 90.00 90.00 120.00 P 31 2 1 6 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 0.017094 0.009869 0.000000 0.00000 SCALE2 0.000000 0.019738 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010002 0.00000