HEADER TRANSPORT PROTEIN 05-DEC-12 4I9R TITLE CRYSTAL STRUCTURE OF THE R111K:R132L:Y134F:T54V:R59W:A32W MUTANT OF TITLE 2 THE CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II IN COMPLEX WITH TITLE 3 ALL-TRANS RETINAL AT 2.6 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR RETINOIC ACID-BINDING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELLULAR RETINOIC ACID-BINDING PROTEIN II, CRABP-II; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS PROTEIN ENGINEERING, WAVELENGTH REGULATION, PH SENSING, PKA, KEYWDS 2 RETINYLIDENE PSB, IMINIUM, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.NOSRATI,J.H.GEIGER REVDAT 4 20-SEP-23 4I9R 1 REMARK SEQADV LINK REVDAT 3 31-JAN-18 4I9R 1 REMARK REVDAT 2 19-FEB-14 4I9R 1 JRNL REVDAT 1 09-OCT-13 4I9R 0 JRNL AUTH T.BERBASOVA,M.NOSRATI,C.VASILEIOU,W.WANG,K.S.LEE,I.YAPICI, JRNL AUTH 2 J.H.GEIGER,B.BORHAN JRNL TITL RATIONAL DESIGN OF A COLORIMETRIC PH SENSOR FROM A SOLUBLE JRNL TITL 2 RETINOIC ACID CHAPERONE. JRNL REF J.AM.CHEM.SOC. V. 135 16111 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 24059243 JRNL DOI 10.1021/JA404900K REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 6726 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 335 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 36.8816 - 3.2757 0.99 3331 174 0.1799 0.2555 REMARK 3 2 3.2757 - 2.6002 0.97 3060 161 0.2539 0.3513 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 64.33 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.750 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.200 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) : -1.19260 REMARK 3 B22 (A**2) : -1.19260 REMARK 3 B33 (A**2) : 2.38510 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1143 REMARK 3 ANGLE : 1.255 1581 REMARK 3 CHIRALITY : 0.374 178 REMARK 3 PLANARITY : 0.011 203 REMARK 3 DIHEDRAL : 17.861 417 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -35.2991 15.0502 13.2069 REMARK 3 T TENSOR REMARK 3 T11: 0.3966 T22: 0.2184 REMARK 3 T33: 0.3179 T12: 0.1444 REMARK 3 T13: -0.0586 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 4.7725 L22: 4.3780 REMARK 3 L33: 3.2830 L12: -2.8720 REMARK 3 L13: 0.3352 L23: -1.0800 REMARK 3 S TENSOR REMARK 3 S11: -0.2884 S12: -0.0437 S13: 0.5069 REMARK 3 S21: 0.4053 S22: 0.0678 S23: -0.3931 REMARK 3 S31: -0.4659 S32: -0.1445 S33: 0.1443 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 4I9R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000076482. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 1.0333 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6726 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 36.878 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2G7B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.5, 2% PEG400, VAPOR REMARK 280 DIFFUSION, SITTING 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 36.59967 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 73.19933 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 73.19933 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 36.59967 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 8 CG CD CE NZ REMARK 470 LYS A 38 CG CD CE NZ REMARK 470 LYS A 44 CG CD CE NZ REMARK 470 GLU A 46 CG CD OE1 OE2 REMARK 470 LYS A 82 CG CD CE NZ REMARK 470 LYS A 98 CG CD CE NZ 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 GLU A 62 CD REMARK 480 GLU A 96 CD 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 VAL A 33 16.42 -62.08 REMARK 500 ALA A 34 -120.24 -87.05 REMARK 500 SER A 37 -2.01 -148.67 REMARK 500 THR A 56 -151.69 -102.08 REMARK 500 GLU A 73 -151.57 -153.71 REMARK 500 ASP A 126 -111.25 49.00 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 RET A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2G7B RELATED DB: PDB REMARK 900 RELATED ID: 2G78 RELATED DB: PDB REMARK 900 RELATED ID: 2FR3 RELATED DB: PDB REMARK 900 RELATED ID: 3F8A RELATED DB: PDB REMARK 900 RELATED ID: 4EXZ RELATED DB: PDB REMARK 900 RELATED ID: 4EEJ RELATED DB: PDB REMARK 900 RELATED ID: 4EFG RELATED DB: PDB REMARK 900 RELATED ID: 3FEP RELATED DB: PDB REMARK 900 RELATED ID: 4I9S RELATED DB: PDB DBREF 4I9R A 1 137 UNP P29373 RABP2_HUMAN 2 138 SEQADV 4I9R TRP A 32 UNP P29373 ALA 33 ENGINEERED MUTATION SEQADV 4I9R VAL A 54 UNP P29373 THR 55 ENGINEERED MUTATION SEQADV 4I9R TRP A 59 UNP P29373 ARG 60 ENGINEERED MUTATION SEQADV 4I9R LYS A 111 UNP P29373 ARG 112 ENGINEERED MUTATION SEQADV 4I9R LEU A 132 UNP P29373 ARG 133 ENGINEERED MUTATION SEQADV 4I9R 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 TRP VAL ALA ALA ALA SER LYS PRO 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 TRP 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 LEU THR MET THR ALA ASP ASP VAL VAL CYS SEQRES 11 A 137 THR LEU VAL PHE VAL ARG GLU HET RET A 201 20 HETNAM RET RETINAL FORMUL 2 RET C20 H28 O FORMUL 3 HOH *11(H2 O) HELIX 1 1 ASN A 14 GLY A 23 1 10 HELIX 2 2 ASN A 25 VAL A 33 1 9 SHEET 1 A10 THR A 60 LYS A 66 0 SHEET 2 A10 THR A 49 SER A 55 -1 N PHE A 50 O PHE A 65 SHEET 3 A10 ALA A 40 GLU A 46 -1 N GLU A 42 O LYS A 53 SHEET 4 A10 GLY A 5 GLU A 13 -1 N TRP A 7 O VAL A 41 SHEET 5 A10 VAL A 128 ARG A 136 -1 O VAL A 133 N ILE A 10 SHEET 6 A10 GLU A 118 ALA A 125 -1 N LEU A 119 O PHE A 134 SHEET 7 A10 THR A 107 LEU A 113 -1 N GLU A 112 O ILE A 120 SHEET 8 A10 LYS A 92 LEU A 99 -1 N CYS A 95 O TRP A 109 SHEET 9 A10 PRO A 80 SER A 89 -1 N LYS A 86 O VAL A 94 SHEET 10 A10 PHE A 71 GLN A 74 -1 N PHE A 71 O SER A 83 LINK NZ LYS A 111 C15 RET A 201 1555 1555 1.26 SITE 1 AC1 9 PHE A 15 MET A 27 TRP A 32 PRO A 39 SITE 2 AC1 9 ILE A 52 TRP A 109 LYS A 111 LEU A 121 SITE 3 AC1 9 MET A 123 CRYST1 57.483 57.483 109.799 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 0.017396 0.010044 0.000000 0.00000 SCALE2 0.000000 0.020088 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009108 0.00000