HEADER TRANSPORT PROTEIN 19-FEB-15 4YCE TITLE CRYSTAL STRUCTURE OF THE R111K:Y134F:T54V:R132Q:P39Q:R59Y MUTANT OF TITLE 2 HUMAN CELLULAR RETINOIC ACID BINDING PROTEINII WITH RETINAL AT 1.95 TITLE 3 ANGSTROM- VISIBLE LIGHT IRRADIATED CRYSTAL FOR 1 HOUR - 2ND CYCLE 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS PROTEIN ENGINEERING, PHOTO SWITCHABLE PROTEINS, RETINAL KEYWDS 2 ISOMERIZATION, RETINAL PROTONATED SCHIFF BASE PKA CHANGE, TRANSPORT KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.NOSRATI,J.H.GEIGER REVDAT 5 27-SEP-23 4YCE 1 REMARK REVDAT 4 03-AUG-16 4YCE 1 JRNL REVDAT 3 29-JUN-16 4YCE 1 JRNL REVDAT 2 15-JUN-16 4YCE 1 TITLE REVDAT 1 24-FEB-16 4YCE 0 JRNL AUTH M.NOSRATI,T.BERBASOVA,C.VASILEIOU,B.BORHAN,J.H.GEIGER JRNL TITL A PHOTOISOMERIZING RHODOPSIN MIMIC OBSERVED AT ATOMIC JRNL TITL 2 RESOLUTION. JRNL REF J.AM.CHEM.SOC. V. 138 8802 2016 JRNL REFN ESSN 1520-5126 JRNL PMID 27310917 JRNL DOI 10.1021/JACS.6B03681 REMARK 2 REMARK 2 RESOLUTION. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 14878 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 754 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 35.5964 - 3.3380 1.00 2991 141 0.1735 0.2010 REMARK 3 2 3.3380 - 2.6497 1.00 2840 143 0.1896 0.2860 REMARK 3 3 2.6497 - 2.3149 0.99 2779 150 0.2097 0.2531 REMARK 3 4 2.3149 - 2.1032 1.00 2755 173 0.2066 0.2401 REMARK 3 5 2.1032 - 1.9525 0.99 2759 147 0.2261 0.2655 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 : 36.77 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.110 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) : 0.50780 REMARK 3 B22 (A**2) : 0.50780 REMARK 3 B33 (A**2) : -1.01560 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 : 0.007 1163 REMARK 3 ANGLE : 1.106 1580 REMARK 3 CHIRALITY : 0.075 183 REMARK 3 PLANARITY : 0.007 205 REMARK 3 DIHEDRAL : 17.174 449 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 4YCE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207196. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9787 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14985 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.9400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : 0.44600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.690 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: 2G7B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG3350, 8% TACSIMATE PH 6.0, REMARK 280 VAPOR DIFFUSION, 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 33.28467 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 66.56933 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 66.56933 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 33.28467 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: 3220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13660 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -33.28467 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 OD2 ASP A 48 O HOH A 301 2.01 REMARK 500 OD1 ASP A 48 O HOH A 302 2.07 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 THR A 56 -163.49 -126.11 REMARK 500 GLU A 73 -153.10 -146.61 REMARK 500 SER A 89 -167.34 -170.17 REMARK 500 ASP A 126 -108.88 52.76 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: 4YBP RELATED DB: PDB REMARK 900 RELATED ID: 2G7B RELATED DB: PDB REMARK 900 RELATED ID: 4I9R RELATED DB: PDB REMARK 900 RELATED ID: 4RUU RELATED DB: PDB REMARK 900 RELATED ID: 4EEJ RELATED DB: PDB REMARK 900 RELATED ID: 4YBU RELATED DB: PDB REMARK 900 RELATED ID: 4YCH RELATED DB: PDB DBREF 4YCE A 1 137 UNP P29373 RABP2_HUMAN 2 138 SEQADV 4YCE GLN A 39 UNP P29373 PRO 40 ENGINEERED MUTATION SEQADV 4YCE VAL A 54 UNP P29373 THR 55 ENGINEERED MUTATION SEQADV 4YCE TYR A 59 UNP P29373 ARG 60 ENGINEERED MUTATION SEQADV 4YCE LYS A 111 UNP P29373 ARG 112 ENGINEERED MUTATION SEQADV 4YCE GLN A 132 UNP P29373 ARG 133 ENGINEERED MUTATION SEQADV 4YCE 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 GLN 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 LEU THR MET THR ALA ASP ASP VAL VAL CYS SEQRES 11 A 137 THR GLN VAL PHE VAL ARG GLU HET RET A 201 20 HETNAM RET RETINAL FORMUL 2 RET C20 H28 O FORMUL 3 HOH *161(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 133 N ILE A 10 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 LYS A 82 O LYS A 98 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 201 1555 1555 1.27 SITE 1 AC1 10 MET A 27 GLN A 39 ILE A 52 VAL A 54 SITE 2 AC1 10 THR A 56 VAL A 76 TRP A 109 LYS A 111 SITE 3 AC1 10 LEU A 121 MET A 123 CRYST1 58.599 58.599 99.854 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 0.017065 0.009853 0.000000 0.00000 SCALE2 0.000000 0.019705 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010015 0.00000