HEADER CHAPERONE 06-SEP-06 2I9S TITLE THE SOLUTION STRUCTURE OF THE CORE OF MESODERM DEVELOPMENT (MESD). CAVEAT 2I9S CHIRALITY ERROR AT ILE36A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: MESODERM DEVELOPMENT CANDIDATE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: P89-K184 CORE REGION; COMPND 5 SYNONYM: MESD; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MESDC2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-30 XA/LIC KEYWDS FERREDOXIN-LIKE-FOLD, CHAPERONE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.KOEHLER,O.ANDERSEN,A.DIEHL,P.SCHMIEDER,G.KRAUSE,H.OSCHKINAT REVDAT 4 09-MAR-22 2I9S 1 REMARK SEQADV REVDAT 3 24-FEB-09 2I9S 1 VERSN REVDAT 2 24-JUL-07 2I9S 1 JRNL REVDAT 1 01-MAY-07 2I9S 0 JRNL AUTH C.KOHLER,O.M.ANDERSEN,A.DIEHL,G.KRAUSE,P.SCHMIEDER, JRNL AUTH 2 H.OSCHKINAT JRNL TITL THE SOLUTION STRUCTURE OF THE CORE OF MESODERM DEVELOPMENT JRNL TITL 2 (MESD), A CHAPERONE FOR MEMBERS OF THE LDLR-FAMILY JRNL REF J.STRUCT.FUNCT.GENOM. V. 7 131 2006 JRNL REFN ISSN 1345-711X JRNL PMID 17342452 JRNL DOI 10.1007/S10969-007-9016-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, X-PLOR 2.15 REMARK 3 AUTHORS : BRUKER BIOSPIN (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON 822 REMARK 3 INTERRESIDUAL DISTANCE RESTRAINTS, 146 DIHEDRAL ANGLE RESTRAINTS REMARK 3 (TALOS) AND 84 HYDROGEN BOND RESTRAINTS. REMARK 4 REMARK 4 2I9S COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039316. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 50MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM MESD_89_184 U-15N,13C, 20MM REMARK 210 PHOSPHATE BUFFER PH 5,5, 50MM REMARK 210 NACL, 0,1MM EDTA, 0,2% NAN3, 90% REMARK 210 H2O, 10% D2O; 1MM MESD_89_184 U- REMARK 210 15N, 20MM PHOSPHATE BUFFER PH 5, REMARK 210 5, 50MM NACL, 0,1MM EDTA, 0,2% REMARK 210 NAN3, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AV REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, TOPSPIN 1.5, SPARKY REMARK 210 3.106, CYANA 2.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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: 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 LEU A 65 HB2 ALA A 71 1.10 REMARK 500 HG23 VAL A 24 HB2 ASP A 82 1.20 REMARK 500 HB THR A 23 HB3 GLU A 86 1.20 REMARK 500 HG12 VAL A 51 HA LEU A 65 1.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 11 LYS A 31 N LYS A 31 CA -0.161 REMARK 500 14 LYS A 31 N LYS A 31 CA -0.200 REMARK 500 18 ILE A 36 N ILE A 36 CA -0.150 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 11 SER A 58 N - CA - CB ANGL. DEV. = -9.4 DEGREES REMARK 500 13 LEU A 65 CB - CA - C ANGL. DEV. = -12.0 DEGREES 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 LYS A 13 -166.60 45.93 REMARK 500 1 SER A 25 33.01 -142.69 REMARK 500 1 PRO A 28 28.89 -76.67 REMARK 500 1 THR A 29 -157.13 -137.78 REMARK 500 1 ARG A 66 -59.09 -120.98 REMARK 500 1 ASP A 67 -9.25 -46.18 REMARK 500 1 SER A 69 43.43 -149.34 REMARK 500 1 TYR A 70 -3.85 -173.49 REMARK 500 1 ARG A 83 -81.97 73.46 REMARK 500 1 CYS A 84 89.05 159.60 REMARK 500 1 ALA A 85 -78.86 -109.31 REMARK 500 1 MET A 93 95.07 55.84 REMARK 500 1 PRO A 95 26.56 -78.95 REMARK 500 2 GLU A 6 10.69 83.56 REMARK 500 2 LYS A 13 149.12 173.38 REMARK 500 2 SER A 25 -48.78 71.26 REMARK 500 2 ASP A 50 71.74 59.70 REMARK 500 2 ASP A 59 9.98 82.47 REMARK 500 2 SER A 69 44.34 -151.99 REMARK 500 2 TYR A 70 16.75 178.99 REMARK 500 2 ASP A 82 -82.52 -176.23 REMARK 500 2 ALA A 85 -51.12 -149.37 REMARK 500 3 GLU A 6 67.32 -106.66 REMARK 500 3 MET A 11 -24.24 79.98 REMARK 500 3 THR A 12 8.06 147.93 REMARK 500 3 LYS A 14 -97.79 -151.09 REMARK 500 3 SER A 25 29.49 -140.84 REMARK 500 3 ASP A 59 9.08 85.25 REMARK 500 3 SER A 69 38.93 -143.06 REMARK 500 3 TYR A 70 -176.18 -179.56 REMARK 500 3 ALA A 71 -30.89 98.06 REMARK 500 3 ASP A 82 -104.35 -155.02 REMARK 500 3 ALA A 85 -40.33 -154.82 REMARK 500 3 MET A 93 4.89 82.81 REMARK 500 4 PRO A 5 -152.87 -77.33 REMARK 500 4 GLU A 6 8.65 82.92 REMARK 500 4 LYS A 13 110.24 -164.80 REMARK 500 4 THR A 29 -105.08 -131.89 REMARK 500 4 GLU A 30 15.74 -167.19 REMARK 500 4 TRP A 40 -76.58 -62.44 REMARK 500 4 TYR A 49 1.60 -67.51 REMARK 500 4 SER A 58 -71.10 -39.02 REMARK 500 4 ARG A 66 -68.61 -105.13 REMARK 500 4 TYR A 70 137.96 175.13 REMARK 500 4 ALA A 71 -33.30 169.27 REMARK 500 4 ASP A 82 -94.14 -163.72 REMARK 500 4 ALA A 85 -36.71 -153.79 REMARK 500 5 THR A 12 36.66 71.34 REMARK 500 5 LYS A 13 -98.44 -91.74 REMARK 500 5 PRO A 28 30.84 -88.36 REMARK 500 REMARK 500 THIS ENTRY HAS 228 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2I9S A 2 97 UNP Q9ERE7 MESD2_MOUSE 89 184 SEQADV 2I9S GLY A 1 UNP Q9ERE7 CLONING ARTIFACT SEQRES 1 A 97 GLY PRO GLY LYS PRO GLU SER ILE LEU LYS MET THR LYS SEQRES 2 A 97 LYS GLY LYS THR LEU MET MET PHE VAL THR VAL SER GLY SEQRES 3 A 97 ASN PRO THR GLU LYS GLU THR GLU GLU ILE THR SER LEU SEQRES 4 A 97 TRP GLN GLY SER LEU PHE ASN ALA ASN TYR ASP VAL GLN SEQRES 5 A 97 ARG PHE ILE VAL GLY SER ASP ARG ALA ILE PHE MET LEU SEQRES 6 A 97 ARG ASP GLY SER TYR ALA TRP GLU ILE LYS ASP PHE LEU SEQRES 7 A 97 VAL SER GLN ASP ARG CYS ALA GLU VAL THR LEU GLU GLY SEQRES 8 A 97 GLN MET TYR PRO GLY LYS HELIX 1 1 PRO A 5 LYS A 13 1 9 HELIX 2 2 THR A 29 ALA A 47 1 19 HELIX 3 3 TYR A 70 ASP A 82 1 13 SHEET 1 A 3 VAL A 51 GLN A 52 0 SHEET 2 A 3 ARG A 60 LEU A 65 -1 O MET A 64 N GLN A 52 SHEET 3 A 3 ILE A 55 GLY A 57 -1 N GLY A 57 O ARG A 60 SHEET 1 B 4 VAL A 51 GLN A 52 0 SHEET 2 B 4 ARG A 60 LEU A 65 -1 O MET A 64 N GLN A 52 SHEET 3 B 4 LEU A 18 THR A 23 -1 N VAL A 22 O ALA A 61 SHEET 4 B 4 GLU A 86 THR A 88 -1 O GLU A 86 N THR A 23 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