HEADER TRANSPORT PROTEIN 21-FEB-15 4YDA
TITLE CRYSTAL STRUCTURE OF R111K:Y134F:T54V:R132Q:P39Q:R59Y MUTANT OF HUMAN
TITLE 2 CELLULAR RETINOIC ACID BINDING PROTEINII WITH RETINAL AT 1.95
TITLE 3 ANGSTROM - AFTER 1HOUR VISIBLE LIGHT IRRADIATION - 3RD 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 PHOTO SWITCHABLE PROTEIN, RETINAL ISOMERIZATION, PKA CHANGE OF
KEYWDS 2 RETINAL PSB, PROTEIN ENGINEERING, RHODOPSIN MIMIC, TRANSPORT PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR M.NOSRATI,J.H.GEIGER
REVDAT 5 27-SEP-23 4YDA 1 REMARK
REVDAT 4 03-AUG-16 4YDA 1 JRNL
REVDAT 3 29-JUN-16 4YDA 1 JRNL
REVDAT 2 15-JUN-16 4YDA 1 TITLE
REVDAT 1 24-FEB-16 4YDA 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) : 45.17
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.200
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 3 NUMBER OF REFLECTIONS : 14837
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.194
REMARK 3 R VALUE (WORKING SET) : 0.192
REMARK 3 FREE R VALUE : 0.241
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050
REMARK 3 FREE R VALUE TEST SET COUNT : 750
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 45.1822 - 3.3354 1.00 2987 139 0.1713 0.2151
REMARK 3 2 3.3354 - 2.6475 0.99 2814 156 0.1928 0.2501
REMARK 3 3 2.6475 - 2.3129 0.99 2780 151 0.2130 0.2607
REMARK 3 4 2.3129 - 2.1014 0.99 2756 151 0.2076 0.2472
REMARK 3 5 2.1014 - 1.9508 0.99 2750 153 0.2447 0.2869
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 : 0.35
REMARK 3 B_SOL : 40.87
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.500
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.750
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) : 0.63800
REMARK 3 B22 (A**2) : 0.63800
REMARK 3 B33 (A**2) : -1.27610
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 : 0.008 1162
REMARK 3 ANGLE : 1.201 1577
REMARK 3 CHIRALITY : 0.077 182
REMARK 3 PLANARITY : 0.005 203
REMARK 3 DIHEDRAL : 15.428 446
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 4YDA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-15.
REMARK 100 THE DEPOSITION ID IS D_1000207250.
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 : 14966
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 (%) : 99.4
REMARK 200 DATA REDUNDANCY : 10.40
REMARK 200 R MERGE (I) : 0.09800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.6900
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 (%) : 99.0
REMARK 200 DATA REDUNDANCY IN SHELL : 7.20
REMARK 200 R MERGE FOR SHELL (I) : 0.57300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000
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 (%): 61.19
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG3350, 8% TACSIMATE PH 6.0,
REMARK 280 VAPOR 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 33.22933
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 66.45867
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 66.45867
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 33.22933
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: 3290 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 13690 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 0.00000
REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 33.22933
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 OE1 GLU A 96 O HOH A 403 2.16
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 ASN A 2 54.64 -105.27
REMARK 500 THR A 56 -164.88 -127.38
REMARK 500 THR A 56 -164.85 -127.57
REMARK 500 GLU A 73 -150.41 -148.92
REMARK 500 SER A 89 -164.39 -167.83
REMARK 500 ASP A 126 -115.48 54.30
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: 4YBU RELATED DB: PDB
REMARK 900 RELATED ID: 4I9S RELATED DB: PDB
REMARK 900 RELATED ID: 2G7B RELATED DB: PDB
REMARK 900 RELATED ID: 4RUU RELATED DB: PDB
REMARK 900 RELATED ID: 4EEJ RELATED DB: PDB
REMARK 900 RELATED ID: 4YCE RELATED DB: PDB
REMARK 900 RELATED ID: 4YCH RELATED DB: PDB
REMARK 900 RELATED ID: 4YDB RELATED DB: PDB
DBREF 4YDA A 1 137 UNP P29373 RABP2_HUMAN 2 138
SEQADV 4YDA GLN A 39 UNP P29373 PRO 40 ENGINEERED MUTATION
SEQADV 4YDA VAL A 54 UNP P29373 THR 55 ENGINEERED MUTATION
SEQADV 4YDA TYR A 59 UNP P29373 ARG 60 ENGINEERED MUTATION
SEQADV 4YDA LYS A 111 UNP P29373 ARG 112 ENGINEERED MUTATION
SEQADV 4YDA GLN A 132 UNP P29373 ARG 133 ENGINEERED MUTATION
SEQADV 4YDA 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 *140(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 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 201 1555 1555 1.27
SITE 1 AC1 9 MET A 27 GLN A 39 ILE A 52 THR A 56
SITE 2 AC1 9 VAL A 76 TRP A 109 LYS A 111 LEU A 121
SITE 3 AC1 9 MET A 123
CRYST1 58.509 58.509 99.688 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 0.017091 0.009868 0.000000 0.00000
SCALE2 0.000000 0.019735 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010031 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
