HEADER TRANSPORT PROTEIN 24-APR-15 4ZH9 TITLE CRYSTAL STRUCTURE OF THE DOMAIN-SWAPPED DIMER WILD-TYPE OF HUMAN TITLE 2 CELLULAR RETINOL BINDING PROTEIN II COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOL-BINDING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELLULAR RETINOL-BINDING PROTEIN II,CRBP-II; COMPND 5 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: RBP2, CRBP2; 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 DOMAIN SWAPPED DIMER, DOMAIN SWAPPING, PROTEIN FOLDING, HUMAN KEYWDS 2 CELLULAR RETINOL BINDING PROTEIN II, INTRA CELLULAR RETINOL BINDING KEYWDS 3 PROTEIN II, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.ASSAR,Z.NOSSONI,J.H.GEIGER REVDAT 5 27-SEP-23 4ZH9 1 REMARK REVDAT 4 25-DEC-19 4ZH9 1 REMARK REVDAT 3 01-NOV-17 4ZH9 1 REMARK REVDAT 2 06-SEP-17 4ZH9 1 JRNL REMARK REVDAT 1 08-JUN-16 4ZH9 0 JRNL AUTH Z.ASSAR,Z.NOSSONI,W.WANG,E.M.SANTOS,K.KRAMER,C.MCCORNACK, JRNL AUTH 2 C.VASILEIOU,B.BORHAN,J.H.GEIGER JRNL TITL DOMAIN-SWAPPED DIMERS OF INTRACELLULAR LIPID-BINDING JRNL TITL 2 PROTEINS: EVIDENCE FOR ORDERED FOLDING INTERMEDIATES. JRNL REF STRUCTURE V. 24 1590 2016 JRNL REFN ISSN 1878-4186 JRNL PMID 27524203 JRNL DOI 10.1016/J.STR.2016.05.022 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.NOSSONI,Z.ASSAR,I.YAPICI,M.NOSRATI,W.WANG,T.BERBASOVA, REMARK 1 AUTH 2 C.VASILEIOU,B.BORHAN,J.GEIGER REMARK 1 TITL STRUCTURES OF HOLO WILD-TYPE HUMAN CELLULAR RETINOL-BINDING REMARK 1 TITL 2 PROTEIN II (HCRBPII) BOUND TO RETINOL AND RETINAL. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 70 3226 2014 REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 25478840 REMARK 1 DOI 10.1107/S1399004714023839 REMARK 1 REFERENCE 2 REMARK 1 AUTH W.WANG,Z.NOSSONI,T.BERBASOVA,C.T.WATSON,I.YAPICI,K.S.LEE, REMARK 1 AUTH 2 C.VASILEIOU,J.H.GEIGER,B.BORHAN REMARK 1 TITL TUNING THE ELECTRONIC ABSORPTION OF PROTEIN-EMBEDDED REMARK 1 TITL 2 ALL-TRANS-RETINAL. REMARK 1 REF SCIENCE V. 338 1340 2012 REMARK 1 REFN ESSN 1095-9203 REMARK 1 PMID 23224553 REMARK 1 DOI 10.1126/SCIENCE.1226135 REMARK 2 REMARK 2 RESOLUTION. 2.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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 : LS_WUNIT_K1 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 4417 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.190 REMARK 3 FREE R VALUE TEST SET COUNT : 450 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 43.9890 - 3.8353 0.99 1369 157 0.1672 0.2512 REMARK 3 2 3.8353 - 3.0445 1.00 1310 149 0.1994 0.2681 REMARK 3 3 3.0445 - 2.6597 1.00 1288 144 0.2961 0.3424 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.060 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 : 0.002 1095 REMARK 3 ANGLE : 0.472 1477 REMARK 3 CHIRALITY : 0.016 161 REMARK 3 PLANARITY : 0.002 192 REMARK 3 DIHEDRAL : 11.281 396 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): 2.7298 36.4241 -2.9222 REMARK 3 T TENSOR REMARK 3 T11: 0.2493 T22: 0.4037 REMARK 3 T33: 0.2147 T12: -0.0035 REMARK 3 T13: -0.0253 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: -0.2588 L22: 2.9345 REMARK 3 L33: 0.0975 L12: -0.2521 REMARK 3 L13: -0.1678 L23: -0.4903 REMARK 3 S TENSOR REMARK 3 S11: 0.0335 S12: 0.0230 S13: -0.0111 REMARK 3 S21: -0.0163 S22: -0.1083 S23: 0.0432 REMARK 3 S31: 0.0013 S32: 0.0417 S33: 0.0827 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 4ZH9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000209277. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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) : 0.978 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4455 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.660 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.4100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.73100 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: PHENIX REMARK 200 STARTING MODEL: 2RCT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 4000 (40%), 0.1M SODIUM REMARK 280 ACETATE PH 4.5, AMMONIUM ACETATE 0.1M, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.27200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.01050 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.27200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.01050 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 300 REMARK: DIMER CONFIRMED BY GEL FILTRATION 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 60.54400 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 227 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 228 LIES ON A SPECIAL POSITION. 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 GLU A 9 CG CD OE1 OE2 REMARK 470 LYS A 31 CG CD CE NZ REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 GLU A 102 CG CD OE1 OE2 REMARK 470 LYS A 131 CG CD CE NZ 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 PHE A 57 118.25 -161.97 REMARK 500 ASN A 59 -141.29 -142.40 REMARK 500 TYR A 60 99.62 -38.05 REMARK 500 LEU A 77 -99.23 -138.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ZH6 RELATED DB: PDB REMARK 900 RELATED ID: 4QZU RELATED DB: PDB REMARK 900 RELATED ID: 4QZT RELATED DB: PDB REMARK 900 RELATED ID: 4QYN RELATED DB: PDB REMARK 900 RELATED ID: 4QYP RELATED DB: PDB DBREF 4ZH9 A 1 133 UNP P50120 RET2_HUMAN 2 134 SEQRES 1 A 133 THR ARG ASP GLN ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 A 133 GLU ASN PHE GLU GLY TYR MET LYS ALA LEU ASP ILE ASP SEQRES 3 A 133 PHE ALA THR ARG LYS ILE ALA VAL ARG LEU THR GLN THR SEQRES 4 A 133 LYS VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS THR LYS SEQRES 5 A 133 THR THR SER THR PHE ARG ASN TYR ASP VAL ASP PHE THR SEQRES 6 A 133 VAL GLY VAL GLU PHE ASP GLU TYR THR LYS SER LEU ASP SEQRES 7 A 133 ASN ARG HIS VAL LYS ALA LEU VAL THR TRP GLU GLY ASP SEQRES 8 A 133 VAL LEU VAL CYS VAL GLN LYS GLY GLU LYS GLU ASN ARG SEQRES 9 A 133 GLY TRP LYS GLN TRP ILE GLU GLY ASP LYS LEU TYR LEU SEQRES 10 A 133 GLU LEU THR CYS GLY ASP GLN VAL CYS ARG GLN VAL PHE SEQRES 11 A 133 LYS LYS LYS FORMUL 2 HOH *34(H2 O) HELIX 1 AA1 ASN A 15 LEU A 23 1 9 HELIX 2 AA2 ASP A 26 VAL A 34 1 9 SHEET 1 AA1 3 GLY A 6 GLU A 9 0 SHEET 2 AA1 3 THR A 39 ASP A 45 -1 O LYS A 40 N TRP A 8 SHEET 3 AA1 3 ASN A 48 THR A 53 -1 O LYS A 50 N ASP A 43 SHEET 1 AA2 6 PHE A 70 TYR A 73 0 SHEET 2 AA2 6 HIS A 81 GLU A 89 -1 O VAL A 82 N GLU A 72 SHEET 3 AA2 6 VAL A 92 LYS A 98 -1 O VAL A 94 N THR A 87 SHEET 4 AA2 6 ARG A 104 GLU A 111 -1 O GLN A 108 N LEU A 93 SHEET 5 AA2 6 LYS A 114 CYS A 121 -1 O THR A 120 N GLY A 105 SHEET 6 AA2 6 GLN A 124 LYS A 131 -1 O CYS A 126 N LEU A 119 CRYST1 36.851 60.544 64.021 90.00 90.00 90.00 P 2 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 0.027136 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016517 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015620 0.00000