HEADER LIPID BINDING PROTEIN 13-JAN-20 6VIT TITLE THE CRYSTAL STRUCTURE OF APO DOMAIN-SWAPPED DIMER Q108K:T51D:I32C TITLE 2 VARIANT OF HCRBPII WITH AN ENGINEERED DISULFIDE BOND COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOL-BINDING PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CELLULAR RETINOL-BINDING PROTEIN II,CRBP-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: RBP2, CRBP2; SOURCE 6 EXPRESSION_SYSTEM: BACTERIAL EXPRESSION VECTOR PET-11A; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1944663 KEYWDS DOMAIN SWAPPED TRIMER, ILBP, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.GHANBARPOUR,J.GEIGER REVDAT 4 16-OCT-24 6VIT 1 REMARK REVDAT 3 11-OCT-23 6VIT 1 REMARK REVDAT 2 05-MAY-21 6VIT 1 JRNL REVDAT 1 19-AUG-20 6VIT 0 JRNL AUTH A.GHANBARPOUR,E.M.SANTOS,C.PINGER,Z.ASSAR,S.HOSSAINI NASR, JRNL AUTH 2 C.VASILEIOU,D.SPENCE,B.BORHAN,J.H.GEIGER JRNL TITL HUMAN CELLULAR RETINOL BINDING PROTEIN II FORMS A JRNL TITL 2 DOMAIN-SWAPPED TRIMER REPRESENTING A NOVEL FOLD AND A NEW JRNL TITL 3 TEMPLATE FOR PROTEIN ENGINEERING. JRNL REF CHEMBIOCHEM V. 21 3192 2020 JRNL REFN ESSN 1439-7633 JRNL PMID 32608180 JRNL DOI 10.1002/CBIC.202000405 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 8636 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 865 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 38.4800 - 5.8200 0.96 1300 149 0.2268 0.2576 REMARK 3 2 5.8200 - 4.6200 0.98 1285 146 0.2272 0.2599 REMARK 3 3 4.6200 - 4.0400 1.00 1322 143 0.2113 0.2932 REMARK 3 4 4.0400 - 3.6700 1.00 1282 145 0.2418 0.3471 REMARK 3 5 3.6700 - 3.4000 1.00 1298 143 0.2616 0.3088 REMARK 3 6 3.4000 - 3.2000 0.99 1284 139 0.2770 0.3421 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) : 0.505 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.048 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 78.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.86 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 : 0.009 2223 REMARK 3 ANGLE : 1.177 2989 REMARK 3 CHIRALITY : 0.062 318 REMARK 3 PLANARITY : 0.006 385 REMARK 3 DIHEDRAL : 20.086 1326 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN 'A' REMARK 3 SELECTION : (CHAIN 'B' AND (RESID 1 THROUGH 127 OR REMARK 3 (RESID 128 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB )) OR RESID 129 REMARK 3 THROUGH 133)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6VIT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000245780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 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) : 0.97624 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8637 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 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 : 5.000 REMARK 200 R MERGE (I) : 0.20000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.10000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2RCT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CITRIC ACID, PEG 3350, PH 6.4, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,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 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.58000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.58000 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 25.58000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLN A 128 CG CD OE1 NE2 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 -92.06 -55.56 REMARK 500 SER A 76 -0.28 73.61 REMARK 500 LEU A 77 -80.62 -127.61 REMARK 500 CYS B 32 -70.34 -89.07 REMARK 500 THR B 54 -48.84 -141.14 REMARK 500 SER B 55 107.50 67.57 REMARK 500 ARG B 58 160.99 64.60 REMARK 500 THR B 74 53.69 -69.86 REMARK 500 SER B 76 -2.06 71.33 REMARK 500 LEU B 77 -76.12 -129.29 REMARK 500 LYS B 132 -177.38 -65.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 6VIT A 1 133 UNP P50120 RET2_HUMAN 2 134 DBREF 6VIT B 1 133 UNP P50120 RET2_HUMAN 2 134 SEQADV 6VIT CYS A 32 UNP P50120 ILE 33 ENGINEERED MUTATION SEQADV 6VIT ASP A 51 UNP P50120 THR 52 ENGINEERED MUTATION SEQADV 6VIT LYS A 108 UNP P50120 GLN 109 ENGINEERED MUTATION SEQADV 6VIT CYS B 32 UNP P50120 ILE 33 ENGINEERED MUTATION SEQADV 6VIT ASP B 51 UNP P50120 THR 52 ENGINEERED MUTATION SEQADV 6VIT LYS B 108 UNP P50120 GLN 109 ENGINEERED MUTATION 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 CYS ALA VAL ARG LEU THR GLN THR SEQRES 4 A 133 LYS VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS ASP 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 LYS 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 SEQRES 1 B 133 THR ARG ASP GLN ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 B 133 GLU ASN PHE GLU GLY TYR MET LYS ALA LEU ASP ILE ASP SEQRES 3 B 133 PHE ALA THR ARG LYS CYS ALA VAL ARG LEU THR GLN THR SEQRES 4 B 133 LYS VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS ASP LYS SEQRES 5 B 133 THR THR SER THR PHE ARG ASN TYR ASP VAL ASP PHE THR SEQRES 6 B 133 VAL GLY VAL GLU PHE ASP GLU TYR THR LYS SER LEU ASP SEQRES 7 B 133 ASN ARG HIS VAL LYS ALA LEU VAL THR TRP GLU GLY ASP SEQRES 8 B 133 VAL LEU VAL CYS VAL GLN LYS GLY GLU LYS GLU ASN ARG SEQRES 9 B 133 GLY TRP LYS LYS TRP ILE GLU GLY ASP LYS LEU TYR LEU SEQRES 10 B 133 GLU LEU THR CYS GLY ASP GLN VAL CYS ARG GLN VAL PHE SEQRES 11 B 133 LYS LYS LYS FORMUL 3 HOH *11(H2 O) HELIX 1 AA1 ASN A 15 ALA A 22 1 8 HELIX 2 AA2 ASP A 26 VAL A 34 1 9 HELIX 3 AA3 ASN B 15 ALA B 22 1 8 HELIX 4 AA4 ASP B 26 VAL B 34 1 9 SHEET 1 AA110 THR B 56 VAL B 62 0 SHEET 2 AA110 ASP A 51 THR A 56 -1 N ASP A 51 O VAL B 62 SHEET 3 AA110 THR A 37 ILE A 42 -1 N THR A 37 O THR A 56 SHEET 4 AA110 GLY A 6 GLU A 14 -1 N TRP A 8 O LYS A 40 SHEET 5 AA110 GLN B 124 LYS B 131 -1 O VAL B 129 N GLU A 11 SHEET 6 AA110 LYS B 114 CYS B 121 -1 N LEU B 119 O CYS B 126 SHEET 7 AA110 GLY B 105 GLU B 111 -1 N TRP B 109 O TYR B 116 SHEET 8 AA110 VAL B 92 LYS B 98 -1 N LEU B 93 O LYS B 108 SHEET 9 AA110 HIS B 81 GLU B 89 -1 N THR B 87 O VAL B 94 SHEET 10 AA110 GLU B 69 TYR B 73 -1 N PHE B 70 O ALA B 84 SHEET 1 AA2 2 GLN A 44 ASP A 45 0 SHEET 2 AA2 2 ASN A 48 PHE A 49 -1 O ASN A 48 N ASP A 45 SHEET 1 AA310 ASP A 61 THR A 65 0 SHEET 2 AA310 ASN B 48 LYS B 52 -1 O ASP B 51 N VAL A 62 SHEET 3 AA310 THR B 39 ASP B 45 -1 N VAL B 41 O LYS B 52 SHEET 4 AA310 GLY B 6 GLU B 14 -1 N TRP B 8 O LYS B 40 SHEET 5 AA310 GLN A 124 LYS A 132 -1 N VAL A 129 O GLU B 11 SHEET 6 AA310 LYS A 114 CYS A 121 -1 N LEU A 119 O CYS A 126 SHEET 7 AA310 GLY A 105 GLU A 111 -1 N TRP A 109 O TYR A 116 SHEET 8 AA310 VAL A 92 GLY A 99 -1 N LEU A 93 O LYS A 108 SHEET 9 AA310 HIS A 81 GLU A 89 -1 N LYS A 83 O LYS A 98 SHEET 10 AA310 GLU A 69 TYR A 73 -1 N PHE A 70 O ALA A 84 SSBOND 1 CYS A 32 CYS B 32 1555 1555 2.04 CRYST1 133.283 133.283 51.160 90.00 90.00 120.00 P 63 12 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 0.007503 0.004332 0.000000 0.00000 SCALE2 0.000000 0.008664 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019547 0.00000