PDB Short entry for 1BM5 HEADER RETINOIC-ACID TRANSPORT 28-JUL-98 1BM5 TITLE THE SOLUTION STRUCTURE OF A SITE-DIRECTED MUTANT (R111M) OF HUMAN TITLE 2 CELLULAR RETIONIC ACID BINDING PROTEIN-TYPE II, NMR, 31 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR RETINOIC ACID BINDING PROTEIN-TYPE II; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: BL21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET-17B KEYWDS RETINOIC-ACID TRANSPORT, CRABPII EXPDTA SOLUTION NMR NUMMDL 31 AUTHOR H.WANG,H.YAN REVDAT 4 16-FEB-22 1BM5 1 REMARK SEQADV REVDAT 3 24-FEB-09 1BM5 1 VERSN REVDAT 2 16-FEB-99 1BM5 1 SOURCE REMARK TITLE JRNL REVDAT 2 2 1 KEYWDS REVDAT 1 13-JAN-99 1BM5 0 JRNL AUTH L.WANG,H.YAN JRNL TITL NMR STUDY SUGGESTS A MAJOR ROLE FOR ARG111 IN MAINTAINING JRNL TITL 2 THE STRUCTURE AND DYNAMICAL PROPERTIES OF TYPE II HUMAN JRNL TITL 3 CELLULAR RETINOIC ACID BINDING PROTEIN. JRNL REF BIOCHEMISTRY V. 37 13021 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9737883 JRNL DOI 10.1021/BI981021X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES WERE CALCULATED REMARK 3 FOLLOWING THE STANDARD DISTANCE GEOMETRY-SIMULATED ANNEALING REMARK 3 PROTOCAL IN X-PLOR 3.1. SEVERAL ROUNDS OF REFINEMENT WERE REMARK 3 PERFORMED. REMARK 4 REMARK 4 1BM5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171903. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7.3 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : PBS REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D HOMONUCLEAR; 3D 15N-EDITED REMARK 210 NMR EXPERIMENTS REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : VXR500; DMX750 REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : DGSA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 75 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 31 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION AND REMARK 210 LOWEST TOTAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 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 1 SER A 12 152.37 177.74 REMARK 500 1 VAL A 24 -34.44 -164.67 REMARK 500 1 ASN A 25 -159.09 -61.71 REMARK 500 1 LYS A 38 73.46 67.34 REMARK 500 1 THR A 56 -71.73 -102.80 REMARK 500 1 THR A 57 -41.52 -172.95 REMARK 500 1 THR A 60 102.96 -164.31 REMARK 500 1 GLU A 62 125.75 -171.87 REMARK 500 1 THR A 75 -144.99 -90.18 REMARK 500 1 GLU A 88 -42.20 -130.99 REMARK 500 1 SER A 89 -153.31 -136.71 REMARK 500 1 ASN A 91 26.84 -147.93 REMARK 500 1 GLU A 103 141.73 -178.94 REMARK 500 1 GLU A 118 172.50 -55.88 REMARK 500 1 ASP A 126 -76.49 78.72 REMARK 500 1 ASP A 127 22.67 -148.25 REMARK 500 2 SER A 12 147.09 177.95 REMARK 500 2 VAL A 24 -40.65 -140.21 REMARK 500 2 ASN A 25 -165.41 -59.74 REMARK 500 2 LYS A 38 72.49 66.37 REMARK 500 2 THR A 56 -80.02 -100.37 REMARK 500 2 THR A 57 -46.43 -158.06 REMARK 500 2 THR A 60 103.47 -163.83 REMARK 500 2 GLU A 62 119.58 -171.94 REMARK 500 2 THR A 75 -152.68 -63.86 REMARK 500 2 GLU A 88 -46.56 -135.11 REMARK 500 2 SER A 89 -152.67 -129.99 REMARK 500 2 ASN A 91 25.27 -143.78 REMARK 500 2 GLU A 103 141.41 -176.26 REMARK 500 2 GLU A 118 171.30 -57.94 REMARK 500 2 ASP A 126 -78.36 77.78 REMARK 500 2 ASP A 127 24.11 -146.57 REMARK 500 3 GLU A 13 24.57 -161.79 REMARK 500 3 ASN A 14 27.82 -161.14 REMARK 500 3 VAL A 24 -39.90 -150.70 REMARK 500 3 ASN A 25 -160.69 -60.80 REMARK 500 3 LYS A 38 74.19 -151.36 REMARK 500 3 THR A 56 -158.87 -99.26 REMARK 500 3 THR A 60 95.44 -163.71 REMARK 500 3 GLU A 62 111.35 -163.34 REMARK 500 3 THR A 75 -142.14 -97.31 REMARK 500 3 GLU A 88 -45.98 -136.69 REMARK 500 3 SER A 89 -153.63 -131.81 REMARK 500 3 ASN A 91 28.53 -143.46 REMARK 500 3 GLU A 103 140.53 -175.96 REMARK 500 3 GLU A 118 173.91 -55.90 REMARK 500 3 ASP A 126 -79.31 77.15 REMARK 500 3 ASP A 127 23.91 -146.19 REMARK 500 4 SER A 12 165.43 176.29 REMARK 500 4 GLU A 13 25.77 -159.32 REMARK 500 REMARK 500 THIS ENTRY HAS 515 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 11 0.28 SIDE CHAIN REMARK 500 1 ARG A 29 0.22 SIDE CHAIN REMARK 500 1 ARG A 59 0.23 SIDE CHAIN REMARK 500 1 ARG A 79 0.26 SIDE CHAIN REMARK 500 1 ARG A 132 0.26 SIDE CHAIN REMARK 500 1 ARG A 136 0.28 SIDE CHAIN REMARK 500 2 ARG A 11 0.31 SIDE CHAIN REMARK 500 2 ARG A 29 0.22 SIDE CHAIN REMARK 500 2 ARG A 59 0.31 SIDE CHAIN REMARK 500 2 ARG A 79 0.31 SIDE CHAIN REMARK 500 2 ARG A 132 0.27 SIDE CHAIN REMARK 500 2 ARG A 136 0.29 SIDE CHAIN REMARK 500 3 ARG A 11 0.29 SIDE CHAIN REMARK 500 3 ARG A 29 0.18 SIDE CHAIN REMARK 500 3 ARG A 59 0.24 SIDE CHAIN REMARK 500 3 ARG A 79 0.23 SIDE CHAIN REMARK 500 3 ARG A 132 0.22 SIDE CHAIN REMARK 500 3 ARG A 136 0.22 SIDE CHAIN REMARK 500 4 ARG A 11 0.29 SIDE CHAIN REMARK 500 4 ARG A 29 0.32 SIDE CHAIN REMARK 500 4 ARG A 59 0.24 SIDE CHAIN REMARK 500 4 ARG A 79 0.28 SIDE CHAIN REMARK 500 4 ARG A 132 0.32 SIDE CHAIN REMARK 500 4 ARG A 136 0.28 SIDE CHAIN REMARK 500 5 ARG A 11 0.32 SIDE CHAIN REMARK 500 5 ARG A 29 0.23 SIDE CHAIN REMARK 500 5 ARG A 59 0.22 SIDE CHAIN REMARK 500 5 ARG A 79 0.22 SIDE CHAIN REMARK 500 5 ARG A 132 0.32 SIDE CHAIN REMARK 500 5 ARG A 136 0.27 SIDE CHAIN REMARK 500 6 ARG A 11 0.28 SIDE CHAIN REMARK 500 6 ARG A 29 0.22 SIDE CHAIN REMARK 500 6 ARG A 59 0.30 SIDE CHAIN REMARK 500 6 ARG A 79 0.30 SIDE CHAIN REMARK 500 6 ARG A 132 0.28 SIDE CHAIN REMARK 500 6 ARG A 136 0.29 SIDE CHAIN REMARK 500 7 ARG A 11 0.24 SIDE CHAIN REMARK 500 7 ARG A 29 0.29 SIDE CHAIN REMARK 500 7 ARG A 59 0.23 SIDE CHAIN REMARK 500 7 ARG A 79 0.30 SIDE CHAIN REMARK 500 7 ARG A 132 0.26 SIDE CHAIN REMARK 500 7 ARG A 136 0.26 SIDE CHAIN REMARK 500 8 ARG A 11 0.25 SIDE CHAIN REMARK 500 8 ARG A 29 0.22 SIDE CHAIN REMARK 500 8 ARG A 59 0.27 SIDE CHAIN REMARK 500 8 ARG A 79 0.23 SIDE CHAIN REMARK 500 8 ARG A 132 0.27 SIDE CHAIN REMARK 500 8 ARG A 136 0.28 SIDE CHAIN REMARK 500 9 ARG A 11 0.28 SIDE CHAIN REMARK 500 9 ARG A 29 0.08 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 186 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1BM5 A 1 137 UNP P29373 RABP2_HUMAN 1 137 SEQADV 1BM5 MET A 111 UNP P29373 ARG 111 CONFLICT 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 PRO SEQRES 4 A 137 ALA VAL GLU ILE LYS GLN GLU GLY ASP THR PHE TYR ILE SEQRES 5 A 137 LYS THR SER THR THR VAL ARG 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 MET 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 ARG VAL TYR VAL ARG GLU HELIX 1 1 PHE A 15 LEU A 22 1 8 HELIX 2 2 MET A 27 ALA A 36 1 10 SHEET 1 A10 THR A 60 LYS A 66 0 SHEET 2 A10 THR A 49 SER A 55 -1 N THR A 54 O THR A 61 SHEET 3 A10 ALA A 40 GLN A 45 -1 N LYS A 44 O TYR A 51 SHEET 4 A10 GLY A 5 GLU A 13 -1 N TRP A 7 O VAL A 41 SHEET 5 A10 THR A 131 VAL A 135 -1 N VAL A 135 O LYS A 8 SHEET 6 A10 LEU A 119 ALA A 125 -1 N LEU A 121 O ARG A 132 SHEET 7 A10 THR A 107 LEU A 113 -1 N GLU A 112 O ILE A 120 SHEET 8 A10 LYS A 92 LEU A 99 -1 N GLN A 97 O THR A 107 SHEET 9 A10 PRO A 80 TRP A 87 -1 N LYS A 86 O VAL A 94 SHEET 10 A10 PHE A 71 GLN A 74 -1 N GLU A 73 O CYS A 81 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000