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 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 MASTER 281 0 0 2 9 0 0 6 0 0 0 11 END