HEADER SIGNALING PROTEIN 11-JAN-00 1DT7 TITLE SOLUTION STRUCTURE OF THE C-TERMINAL NEGATIVE REGULATORY DOMAIN OF P53 TITLE 2 IN A COMPLEX WITH CA2+-BOUND S100B(BB) COMPND MOL_ID: 1; COMPND 2 MOLECULE: S100 CALCIUM-BINDING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: BETA CHAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 8 CHAIN: X, Y; COMPND 9 FRAGMENT: C-TERMINAL PEPTIDE; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 ORGAN: BRAIN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: HMS174(DE3); SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 13 OF THIS PEPTIDE NATURALLY OCCURS IN HUMANS (HOMO SAPIENS). KEYWDS S100B, P53, C-TERMINAL DOMAIN OF P53, CALCIUM-BINDING, EF-HAND, S100 KEYWDS 2 PROTEIN, FOUR HELIX BUNDLE, HELIX LOOP HELIX, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 40 AUTHOR R.R.RUSTANDI,D.M.BALDISSERI,D.J.WEBER REVDAT 5 27-APR-16 1DT7 1 ATOM VERSN REVDAT 4 24-FEB-09 1DT7 1 VERSN REVDAT 3 04-SEP-07 1DT7 1 JRNL REVDAT 2 01-APR-03 1DT7 1 JRNL REVDAT 1 26-JUL-00 1DT7 0 JRNL AUTH R.R.RUSTANDI,D.M.BALDISSERI,D.J.WEBER JRNL TITL STRUCTURE OF THE NEGATIVE REGULATORY DOMAIN OF P53 BOUND TO JRNL TITL 2 S100B(BETABETA). JRNL REF NAT.STRUCT.BIOL. V. 7 570 2000 JRNL REFN ISSN 1072-8368 JRNL PMID 10876243 JRNL DOI 10.1038/76797 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER, A. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DT7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAY-00. REMARK 100 THE RCSB ID CODE IS RCSB010347. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 25 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 3-6 MM S100 (SUBUNIT REMARK 210 CONCENTRATION), 0.1 MM EDTA, 0.34 REMARK 210 MM NAN3, 5 MM DTT, 17 MM NACL, 10 REMARK 210 MM D11-TRIS-HCL, 7% D2O, 6-13 MM REMARK 210 CACL2, 4.8-10 MM P53 PEPTIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 4D_13C-SEPARATED_NOESY; 4D_13C/ REMARK 210 15N-SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_NOESY; 2D NOESY; 3D 13C REMARK 210 -FILTER NOESY; 2D 13C-FILTER NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.0, NMRPIPE, X-PLOR REMARK 210 3.851 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 40 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURE WITH THE LOWEST ENERGY REMARK 210 AND THE LEAST RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 22 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, X, Y 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 (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-40 REMARK 470 RES CSSEQI ATOMS REMARK 470 GLU A 91 C O REMARK 470 GLU B 91 C O REMARK 470 GLU X 113 C O REMARK 470 GLU Y 113 C O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HG SER B 41 HD1 HIS B 42 1.35 REMARK 500 O CYS B 84 H PHE B 88 1.43 REMARK 500 O CYS A 84 H PHE A 88 1.43 REMARK 500 O MET B 57 H ASP B 61 1.50 REMARK 500 O MET A 57 H ASP A 61 1.50 REMARK 500 OE1 GLU B 2 HZ2 LYS B 5 1.51 REMARK 500 OD2 ASP B 61 H GLY B 66 1.60 REMARK 500 OD2 ASP A 61 H GLY A 66 1.60 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 1 SER A 1 19.99 49.18 REMARK 500 1 GLU A 2 26.40 -76.22 REMARK 500 1 HIS A 90 72.34 -69.16 REMARK 500 1 SER B 1 19.98 49.48 REMARK 500 1 GLU B 2 25.59 -76.01 REMARK 500 1 HIS B 90 72.35 -69.26 REMARK 500 1 GLN X 100 116.40 57.19 REMARK 500 1 GLN Y 100 116.16 57.40 REMARK 500 2 GLU A 21 -73.25 -85.74 REMARK 500 2 LEU A 44 -144.54 -136.02 REMARK 500 2 GLU B 21 -73.50 -85.80 REMARK 500 2 LEU B 44 -144.27 -135.69 REMARK 500 2 LYS X 97 88.85 -170.51 REMARK 500 2 LYS Y 97 88.73 -170.56 REMARK 500 3 LEU A 3 -19.66 -46.17 REMARK 500 3 ASP A 23 68.73 -69.92 REMARK 500 3 LYS A 29 -27.21 -38.39 REMARK 500 3 LEU B 3 -19.75 -46.36 REMARK 500 3 ASP B 23 68.89 -69.92 REMARK 500 3 LYS B 29 -27.74 -38.20 REMARK 500 3 LEU X 94 -83.52 -90.03 REMARK 500 3 LYS X 95 -92.37 -153.37 REMARK 500 3 LEU Y 94 -83.16 -89.99 REMARK 500 3 LYS Y 95 -92.48 -153.81 REMARK 500 4 SER A 1 16.53 48.41 REMARK 500 4 LEU A 44 -145.06 -127.80 REMARK 500 4 SER B 1 16.32 48.40 REMARK 500 4 LEU B 44 -145.02 -127.75 REMARK 500 5 GLU A 21 -77.54 -89.99 REMARK 500 5 GLU A 45 106.04 -52.62 REMARK 500 5 GLU B 21 -78.04 -90.03 REMARK 500 5 GLU B 45 106.13 -52.54 REMARK 500 6 SER A 1 12.62 50.07 REMARK 500 6 SER B 1 12.37 50.03 REMARK 500 7 SER A 1 16.80 49.77 REMARK 500 7 LEU A 40 64.03 -103.60 REMARK 500 7 GLU A 89 99.66 -57.15 REMARK 500 7 SER B 1 16.93 49.90 REMARK 500 7 LEU B 40 63.56 -103.50 REMARK 500 7 GLU B 89 99.72 -57.34 REMARK 500 8 ASP A 23 46.97 -68.72 REMARK 500 8 LEU A 40 53.90 -113.33 REMARK 500 8 SER A 41 100.62 -57.94 REMARK 500 8 HIS A 42 -2.65 55.50 REMARK 500 8 LEU A 44 -144.63 -129.76 REMARK 500 8 ASP B 23 47.12 -68.62 REMARK 500 8 LEU B 40 53.92 -113.33 REMARK 500 8 SER B 41 100.70 -57.83 REMARK 500 8 HIS B 42 -2.62 55.43 REMARK 500 8 LEU B 44 -144.74 -129.79 REMARK 500 REMARK 500 THIS ENTRY HAS 248 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 CA A 114 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 18 O REMARK 620 2 ASP A 23 O 91.1 REMARK 620 3 LYS A 26 O 145.0 55.1 REMARK 620 4 GLU A 31 OE1 135.9 113.8 73.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 CA A 115 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 61 OD1 REMARK 620 2 ASP A 63 N 85.4 REMARK 620 3 ASP A 63 OD2 154.5 79.8 REMARK 620 4 ASP A 65 OD1 62.3 122.5 109.2 REMARK 620 5 GLU A 67 O 90.2 174.2 102.9 51.8 REMARK 620 6 GLU A 72 OE1 113.1 76.8 83.7 157.7 108.5 REMARK 620 7 GLU A 72 OE2 154.0 99.4 50.3 130.8 86.2 45.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 CA B 116 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 18 O REMARK 620 2 LYS B 26 O 144.4 REMARK 620 3 GLU B 31 OE1 138.3 74.8 REMARK 620 4 ASP B 23 O 91.1 55.3 116.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 CA B 117 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 61 OD1 REMARK 620 2 ASP B 63 N 84.9 REMARK 620 3 ASP B 63 OD2 153.7 79.5 REMARK 620 4 ASP B 65 OD1 62.1 121.6 109.1 REMARK 620 5 GLU B 67 O 90.6 173.8 103.1 52.3 REMARK 620 6 GLU B 72 OE1 113.0 76.6 83.9 158.6 109.1 REMARK 620 7 GLU B 72 OE2 154.5 99.1 50.4 131.7 86.8 45.2 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 114 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 115 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 116 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 117 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4099 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFT ASSIGNMENT FOR S100B(BB) REMARK 900 RELATED ID: 2169 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFT ASSIGNMENT FOR C-TERMINAL OF P53 PEPTIDE DBREF 1DT7 A 0 91 UNP P04631 S100B_RAT 1 92 DBREF 1DT7 B 0 91 UNP P04631 S100B_RAT 1 92 DBREF 1DT7 X 92 113 UNP P04637 P53_HUMAN 367 388 DBREF 1DT7 Y 92 113 UNP P04637 P53_HUMAN 367 388 SEQRES 1 A 92 MET SER GLU LEU GLU LYS ALA MET VAL ALA LEU ILE ASP SEQRES 2 A 92 VAL PHE HIS GLN TYR SER GLY ARG GLU GLY ASP LYS HIS SEQRES 3 A 92 LYS LEU LYS LYS SER GLU LEU LYS GLU LEU ILE ASN ASN SEQRES 4 A 92 GLU LEU SER HIS PHE LEU GLU GLU ILE LYS GLU GLN GLU SEQRES 5 A 92 VAL VAL ASP LYS VAL MET GLU THR LEU ASP GLU ASP GLY SEQRES 6 A 92 ASP GLY GLU CYS ASP PHE GLN GLU PHE MET ALA PHE VAL SEQRES 7 A 92 SER MET VAL THR THR ALA CYS HIS GLU PHE PHE GLU HIS SEQRES 8 A 92 GLU SEQRES 1 B 92 MET SER GLU LEU GLU LYS ALA MET VAL ALA LEU ILE ASP SEQRES 2 B 92 VAL PHE HIS GLN TYR SER GLY ARG GLU GLY ASP LYS HIS SEQRES 3 B 92 LYS LEU LYS LYS SER GLU LEU LYS GLU LEU ILE ASN ASN SEQRES 4 B 92 GLU LEU SER HIS PHE LEU GLU GLU ILE LYS GLU GLN GLU SEQRES 5 B 92 VAL VAL ASP LYS VAL MET GLU THR LEU ASP GLU ASP GLY SEQRES 6 B 92 ASP GLY GLU CYS ASP PHE GLN GLU PHE MET ALA PHE VAL SEQRES 7 B 92 SER MET VAL THR THR ALA CYS HIS GLU PHE PHE GLU HIS SEQRES 8 B 92 GLU SEQRES 1 X 22 SER HIS LEU LYS SER LYS LYS GLY GLN SER THR SER ARG SEQRES 2 X 22 HIS LYS LYS LEU MET PHE LYS THR GLU SEQRES 1 Y 22 SER HIS LEU LYS SER LYS LYS GLY GLN SER THR SER ARG SEQRES 2 Y 22 HIS LYS LYS LEU MET PHE LYS THR GLU HET CA A 114 1 HET CA A 115 1 HET CA B 116 1 HET CA B 117 1 HETNAM CA CALCIUM ION FORMUL 5 CA 4(CA 2+) HELIX 1 1 GLU A 2 GLY A 19 1 18 HELIX 2 2 LYS A 29 LEU A 40 1 12 HELIX 3 3 GLU A 49 ASP A 61 1 13 HELIX 4 4 PHE A 70 PHE A 88 1 19 HELIX 5 5 GLU B 2 GLY B 19 1 18 HELIX 6 6 LYS B 29 LEU B 40 1 12 HELIX 7 7 GLU B 49 ASP B 61 1 13 HELIX 8 8 PHE B 70 PHE B 88 1 19 HELIX 9 9 GLN X 100 THR X 102 5 3 HELIX 10 10 SER X 103 GLU X 113 1 11 HELIX 11 11 GLN Y 100 THR Y 102 5 3 HELIX 12 12 SER Y 103 GLU Y 113 1 11 SHEET 1 A 2 LYS A 26 LYS A 28 0 SHEET 2 A 2 GLU A 67 ASP A 69 -1 O CYS A 68 N LEU A 27 SHEET 1 B 2 LYS B 26 LYS B 28 0 SHEET 2 B 2 GLU B 67 ASP B 69 -1 O CYS B 68 N LEU B 27 LINK O SER A 18 CA CA A 114 1555 1555 2.81 LINK O ASP A 23 CA CA A 114 1555 1555 2.00 LINK O LYS A 26 CA CA A 114 1555 1555 2.81 LINK OE1 GLU A 31 CA CA A 114 1555 1555 2.61 LINK OD1 ASP A 61 CA CA A 115 1555 1555 2.85 LINK N ASP A 63 CA CA A 115 1555 1555 2.67 LINK OD2 ASP A 63 CA CA A 115 1555 1555 2.88 LINK OD1 ASP A 65 CA CA A 115 1555 1555 2.86 LINK O GLU A 67 CA CA A 115 1555 1555 2.63 LINK OE1 GLU A 72 CA CA A 115 1555 1555 2.81 LINK OE2 GLU A 72 CA CA A 115 1555 1555 2.81 LINK O SER B 18 CA CA B 116 1555 1555 2.82 LINK O LYS B 26 CA CA B 116 1555 1555 2.81 LINK OE1 GLU B 31 CA CA B 116 1555 1555 2.56 LINK OD1 ASP B 61 CA CA B 117 1555 1555 2.86 LINK N ASP B 63 CA CA B 117 1555 1555 2.69 LINK OD2 ASP B 63 CA CA B 117 1555 1555 2.88 LINK OD1 ASP B 65 CA CA B 117 1555 1555 2.85 LINK O GLU B 67 CA CA B 117 1555 1555 2.62 LINK OE1 GLU B 72 CA CA B 117 1555 1555 2.81 LINK OE2 GLU B 72 CA CA B 117 1555 1555 2.80 LINK CA CA B 116 O ASP B 23 1555 1555 1.98 SITE 1 AC1 5 SER A 18 ASP A 23 LYS A 26 LEU A 27 SITE 2 AC1 5 GLU A 31 SITE 1 AC2 7 ASP A 61 GLU A 62 ASP A 63 GLY A 64 SITE 2 AC2 7 ASP A 65 GLU A 67 GLU A 72 SITE 1 AC3 4 SER B 18 ASP B 23 LYS B 26 GLU B 31 SITE 1 AC4 7 ASP B 61 GLU B 62 ASP B 63 GLY B 64 SITE 2 AC4 7 ASP B 65 GLU B 67 GLU B 72 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 MODEL 1 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20 MODEL 21 MODEL 22 MODEL 23 MODEL 24 MODEL 25 MODEL 26 MODEL 27 MODEL 28 MODEL 29 MODEL 30 MODEL 31 MODEL 32 MODEL 33 MODEL 34 MODEL 35 MODEL 36 MODEL 37 MODEL 38 MODEL 39 MODEL 40