HEADER LIPID BINDING PROTEIN 26-AUG-20 7JX2 TITLE CELLULAR RETINOL-BINDING PROTEIN 2 (CRBP2) IN COMPLEX WITH 2- TITLE 2 PALMITOYLGLYCEROL 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_STRAIN: BL21DE KEYWDS PALMITOYLGLYCEROL, MONOACYLGLYCEROL, RETINOL-BINDING PROTEIN, LIPID KEYWDS 2 BINDING, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.A.SILVAROLI,S.BANARJEE,M.GOLCZAK REVDAT 3 18-OCT-23 7JX2 1 REMARK REVDAT 2 07-APR-21 7JX2 1 JRNL REVDAT 1 10-MAR-21 7JX2 0 JRNL AUTH J.A.SILVAROLI,J.PLAU,C.H.ADAMS,S.BANERJEE, JRNL AUTH 2 M.A.K.WIDJAJA-ADHI,W.S.BLANER,M.GOLCZAK JRNL TITL MOLECULAR BASIS FOR THE INTERACTION OF CELLULAR RETINOL JRNL TITL 2 BINDING PROTEIN 2 (CRBP2) WITH NONRETINOID LIGANDS. JRNL REF J.LIPID RES. V. 62 00054 2021 JRNL REFN ISSN 0022-2275 JRNL PMID 33631211 JRNL DOI 10.1016/J.JLR.2021.100054 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 15383 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) : 0.206 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.670 REMARK 3 FREE R VALUE TEST SET COUNT : 719 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 46.3100 - 3.0800 0.99 3081 145 0.1847 0.2315 REMARK 3 2 3.0800 - 2.4400 0.99 2923 145 0.2249 0.2845 REMARK 3 3 2.4400 - 2.1300 0.99 2890 157 0.2058 0.2544 REMARK 3 4 2.1300 - 1.9400 0.99 2896 134 0.2256 0.2700 REMARK 3 5 1.9400 - 1.8000 1.00 2874 138 0.2594 0.3042 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.440 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 : 0.008 1161 REMARK 3 ANGLE : 0.789 1557 REMARK 3 CHIRALITY : 0.048 166 REMARK 3 PLANARITY : 0.003 198 REMARK 3 DIHEDRAL : 10.042 164 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): -4.0167 -10.3064 15.5622 REMARK 3 T TENSOR REMARK 3 T11: 0.1383 T22: 0.1612 REMARK 3 T33: 0.2435 T12: -0.0039 REMARK 3 T13: 0.0050 T23: 0.0136 REMARK 3 L TENSOR REMARK 3 L11: 2.2358 L22: 3.1755 REMARK 3 L33: 2.0004 L12: -0.4939 REMARK 3 L13: -0.8538 L23: 0.5951 REMARK 3 S TENSOR REMARK 3 S11: 0.0419 S12: 0.0413 S13: -0.0455 REMARK 3 S21: -0.1534 S22: -0.0385 S23: 0.1171 REMARK 3 S31: 0.0194 S32: -0.0943 S33: -0.0137 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 7JX2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251505. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15466 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 66.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.87300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: 6BTI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS HCL, PEG 3350 22-28%, PH REMARK 280 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 18.66950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.29000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.22500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.29000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.66950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.22500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 VAL A 135 REMARK 465 PRO A 136 REMARK 465 ARG A 137 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 O HOH A 390 O HOH A 425 1.99 REMARK 500 O HOH A 337 O HOH A 430 2.08 REMARK 500 N THR A 1 O HOH A 301 2.09 REMARK 500 O HOH A 418 O HOH A 475 2.11 REMARK 500 O HOH A 303 O HOH A 447 2.15 REMARK 500 O HOH A 436 O HOH A 451 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE2 HIS A 81 O HOH A 301 1655 1.94 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 SER A 76 -8.33 73.32 REMARK 500 LEU A 77 -104.96 -95.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 507 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 508 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A 509 DISTANCE = 7.27 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue VLP A 201 DBREF 7JX2 A 0 133 UNP P50120 RET2_HUMAN 1 134 SEQADV 7JX2 LEU A 134 UNP P50120 EXPRESSION TAG SEQADV 7JX2 VAL A 135 UNP P50120 EXPRESSION TAG SEQADV 7JX2 PRO A 136 UNP P50120 EXPRESSION TAG SEQADV 7JX2 ARG A 137 UNP P50120 EXPRESSION TAG SEQRES 1 A 138 MET THR ARG ASP GLN ASN GLY THR TRP GLU MET GLU SER SEQRES 2 A 138 ASN GLU ASN PHE GLU GLY TYR MET LYS ALA LEU ASP ILE SEQRES 3 A 138 ASP PHE ALA THR ARG LYS ILE ALA VAL ARG LEU THR GLN SEQRES 4 A 138 THR LYS VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS THR SEQRES 5 A 138 LYS THR THR SER THR PHE ARG ASN TYR ASP VAL ASP PHE SEQRES 6 A 138 THR VAL GLY VAL GLU PHE ASP GLU TYR THR LYS SER LEU SEQRES 7 A 138 ASP ASN ARG HIS VAL LYS ALA LEU VAL THR TRP GLU GLY SEQRES 8 A 138 ASP VAL LEU VAL CYS VAL GLN LYS GLY GLU LYS GLU ASN SEQRES 9 A 138 ARG GLY TRP LYS GLN TRP ILE GLU GLY ASP LYS LEU TYR SEQRES 10 A 138 LEU GLU LEU THR CYS GLY ASP GLN VAL CYS ARG GLN VAL SEQRES 11 A 138 PHE LYS LYS LYS LEU VAL PRO ARG HET VLP A 201 23 HETNAM VLP 1,3-DIHYDROXYPROPAN-2-YL HEXADECANOATE FORMUL 2 VLP C19 H38 O4 FORMUL 3 HOH *209(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 AA110 TYR A 60 THR A 65 0 SHEET 2 AA110 ASN A 48 THR A 54 -1 N PHE A 49 O PHE A 64 SHEET 3 AA110 THR A 39 ASP A 45 -1 N ASP A 43 O LYS A 50 SHEET 4 AA110 GLY A 6 GLU A 14 -1 N GLY A 6 O ILE A 42 SHEET 5 AA110 GLN A 124 LYS A 132 -1 O LYS A 131 N GLU A 9 SHEET 6 AA110 LYS A 114 CYS A 121 -1 N LEU A 119 O CYS A 126 SHEET 7 AA110 ARG A 104 GLU A 111 -1 N TRP A 109 O TYR A 116 SHEET 8 AA110 VAL A 92 LYS A 98 -1 N GLN A 97 O ARG A 104 SHEET 9 AA110 HIS A 81 GLU A 89 -1 N THR A 87 O VAL A 94 SHEET 10 AA110 PHE A 70 TYR A 73 -1 N PHE A 70 O ALA A 84 SITE 1 AC1 12 MET A 20 ILE A 25 THR A 29 ALA A 33 SITE 2 AC1 12 LEU A 36 LYS A 40 THR A 51 THR A 53 SITE 3 AC1 12 SER A 55 VAL A 62 GLN A 108 HOH A 314 CRYST1 37.339 64.450 66.580 90.00 90.00 90.00 P 21 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 0.026781 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015020 0.00000