PDB Short entry for 2K27 HEADER TRANSCRIPTION REGULATOR 26-MAR-08 2K27 TITLE SOLUTION STRUCTURE OF HUMAN PAX8 PAIRED BOX DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAIRED BOX PROTEIN PAX-8; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PAX8 PAIRED BOX DOMAIN (UNP RESIDUES 1-143); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 GENE: PAX8; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21-DE3; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PIVEX2.3; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PLYSS KEYWDS PAIRED DOMAIN, PAX8, SOLUTION STRUCTURE, TRIPLE FREQUENCY, 3D NMR, KEYWDS 2 INDUCED FIT, ALTERNATIVE SPLICING, DEVELOPMENTAL PROTEIN, KEYWDS 3 DIFFERENTIATION, DISEASE MUTATION, DNA-BINDING, NUCLEUS, PAIRED BOX, KEYWDS 4 PHOSPHOPROTEIN, POLYMORPHISM, TRANSCRIPTION, TRANSCRIPTION KEYWDS 5 REGULATION, TRANSCRIPTION REGULATOR EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.CODUTTI,G.ESPOSITO,A.CORAZZA,F.FOGOLARI,G.TELL,C.VASCOTTO,H.VAN AUTHOR 2 INGEN,R.BOELENS,P.VIGLINO,F.QUADRIFOGLIO REVDAT 7 14-JUN-23 2K27 1 REMARK REVDAT 6 19-FEB-20 2K27 1 REMARK SEQADV REVDAT 5 09-JUN-09 2K27 1 REVDAT REVDAT 4 24-FEB-09 2K27 1 VERSN REVDAT 3 23-DEC-08 2K27 1 JRNL REVDAT 2 04-NOV-08 2K27 1 JRNL REVDAT 1 30-SEP-08 2K27 0 JRNL AUTH L.CODUTTI,H.VAN INGEN,C.VASCOTTO,F.FOGOLARI,A.CORAZZA, JRNL AUTH 2 G.TELL,F.QUADRIFOGLIO,P.VIGLINO,R.BOELENS,G.ESPOSITO JRNL TITL THE SOLUTION STRUCTURE OF DNA-FREE PAX-8 PAIRED BOX DOMAIN JRNL TITL 2 ACCOUNTS FOR REDOX REGULATION OF TRANSCRIPTIONAL ACTIVITY IN JRNL TITL 3 THE PAX PROTEIN FAMILY. JRNL REF J.BIOL.CHEM. V. 283 33321 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18829450 JRNL DOI 10.1074/JBC.M805717200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, DISCOVER 2.98 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 ACCELRYS SOFTWARE INC. (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 MINIMIZATION WAS PERFORMED BY MEANS OF DISCOVER, WITH 200 REMARK 3 ITERATIONS USING THE STEEP DESCENT AND 800 ITERATIONS USING THE REMARK 3 CONJUGATE GRADIENTS ALGORITHMS. C-TERMINAL SUPERPOSITION IS REMARK 3 PERFORMED BETWEEN RESIDUES 87-135 AND THE N-TERMINAL SUPERPOSITION REMARK 3 CAN BE PERFORMED BETWEEN 29-62. REMARK 4 REMARK 4 2K27 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000100582. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.00 REMARK 210 PH : 6.2 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.9 MM [U-100% 13C; U-100% 15N] REMARK 210 PAX8 PAIRED BOX DOMAIN, 40 UM REMARK 210 DSS, 50 MM SODIUM PHOSPHATE, 0.1 REMARK 210 % SODIUM AZIDE, 15 MM [U-100% 2H] REMARK 210 DTT, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 CT; 3D CBCA(CO)NH; 3D C(CO)NH; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HN(CO)CA; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 3D REMARK 210 CBCANH; 3D HN(COCA)CB REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; AVANCE 2 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TALOS (NMR-PIPE 3.5), REMARK 210 PROCHECKNMR 3.4, TOPSPIN 1.3, REMARK 210 CARA 1.8.4, AQUA 3.2, WHAT IF REMARK 210 METHOD USED : MOLECULAR MECHANICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 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: 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 ASN A 4 154.42 75.41 REMARK 500 1 LEU A 16 141.56 70.90 REMARK 500 1 ALA A 19 89.61 -60.26 REMARK 500 1 VAL A 21 -83.60 -112.05 REMARK 500 1 SER A 54 -105.84 -82.28 REMARK 500 1 HIS A 55 -45.26 -154.65 REMARK 500 1 TYR A 65 76.58 56.75 REMARK 500 1 TYR A 66 94.07 68.50 REMARK 500 1 THR A 68 48.08 35.43 REMARK 500 1 ILE A 71 62.63 62.86 REMARK 500 1 ARG A 72 66.63 -161.57 REMARK 500 1 LYS A 80 71.79 -154.49 REMARK 500 1 LEU A 142 79.95 -154.09 REMARK 500 1 SER A 153 89.18 -152.86 REMARK 500 2 SER A 5 -66.17 -155.14 REMARK 500 2 GLN A 15 -62.70 -131.32 REMARK 500 2 ASN A 22 96.21 -164.69 REMARK 500 2 PRO A 27 -162.90 -76.14 REMARK 500 2 HIS A 55 -34.84 -143.03 REMARK 500 2 TYR A 65 -66.77 -159.66 REMARK 500 2 TYR A 66 95.68 -160.47 REMARK 500 2 GLN A 98 -70.68 -72.79 REMARK 500 2 PRO A 100 -169.01 -75.30 REMARK 500 2 THR A 121 -59.86 -154.34 REMARK 500 2 SER A 124 115.33 -20.39 REMARK 500 2 LYS A 135 -72.22 -70.30 REMARK 500 3 HIS A 3 -58.51 -154.78 REMARK 500 3 ASN A 4 157.93 69.90 REMARK 500 3 PHE A 20 -80.08 -73.83 REMARK 500 3 CYS A 45 -29.79 167.81 REMARK 500 3 SER A 54 -88.76 -99.06 REMARK 500 3 HIS A 55 -41.01 -143.97 REMARK 500 3 TYR A 65 115.27 78.87 REMARK 500 3 TYR A 66 75.40 51.00 REMARK 500 3 THR A 68 90.21 -51.08 REMARK 500 3 GLN A 137 39.03 -82.07 REMARK 500 3 LEU A 142 89.18 -155.50 REMARK 500 3 SER A 146 36.62 -146.67 REMARK 500 3 HIS A 158 -168.73 -74.47 REMARK 500 4 ASN A 4 163.20 68.69 REMARK 500 4 ALA A 19 -177.65 63.05 REMARK 500 4 VAL A 21 -81.44 -140.08 REMARK 500 4 LEU A 26 -67.93 -156.42 REMARK 500 4 PRO A 27 -159.37 -79.98 REMARK 500 4 GLU A 28 -36.98 -39.58 REMARK 500 4 SER A 54 -69.41 -104.42 REMARK 500 4 HIS A 55 -42.69 -166.10 REMARK 500 4 TYR A 65 -74.40 -94.23 REMARK 500 4 TYR A 66 36.34 -164.14 REMARK 500 4 GLU A 67 -141.97 51.54 REMARK 500 REMARK 500 THIS ENTRY HAS 267 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 119 ASP A 120 18 147.91 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 2 TYR A 65 0.10 SIDE CHAIN REMARK 500 5 TYR A 66 0.10 SIDE CHAIN REMARK 500 8 TYR A 95 0.18 SIDE CHAIN REMARK 500 9 TYR A 65 0.10 SIDE CHAIN REMARK 500 12 TYR A 65 0.07 SIDE CHAIN REMARK 500 13 TYR A 65 0.07 SIDE CHAIN REMARK 500 14 TYR A 95 0.07 SIDE CHAIN REMARK 500 18 ARG A 33 0.08 SIDE CHAIN REMARK 500 18 TYR A 95 0.08 SIDE CHAIN REMARK 500 20 ARG A 43 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15693 RELATED DB: BMRB DBREF 2K27 A 1 143 UNP Q06710 PAX8_HUMAN 1 143 SEQADV 2K27 MET A 144 UNP Q06710 EXPRESSION TAG SEQADV 2K27 ASP A 145 UNP Q06710 EXPRESSION TAG SEQADV 2K27 SER A 146 UNP Q06710 EXPRESSION TAG SEQADV 2K27 GLY A 147 UNP Q06710 EXPRESSION TAG SEQADV 2K27 ALA A 148 UNP Q06710 EXPRESSION TAG SEQADV 2K27 PRO A 149 UNP Q06710 EXPRESSION TAG SEQADV 2K27 GLY A 150 UNP Q06710 EXPRESSION TAG SEQADV 2K27 GLY A 151 UNP Q06710 EXPRESSION TAG SEQADV 2K27 GLY A 152 UNP Q06710 EXPRESSION TAG SEQADV 2K27 SER A 153 UNP Q06710 EXPRESSION TAG SEQADV 2K27 HIS A 154 UNP Q06710 EXPRESSION TAG SEQADV 2K27 HIS A 155 UNP Q06710 EXPRESSION TAG SEQADV 2K27 HIS A 156 UNP Q06710 EXPRESSION TAG SEQADV 2K27 HIS A 157 UNP Q06710 EXPRESSION TAG SEQADV 2K27 HIS A 158 UNP Q06710 EXPRESSION TAG SEQADV 2K27 HIS A 159 UNP Q06710 EXPRESSION TAG SEQRES 1 A 159 MET PRO HIS ASN SER ILE ARG SER GLY HIS GLY GLY LEU SEQRES 2 A 159 ASN GLN LEU GLY GLY ALA PHE VAL ASN GLY ARG PRO LEU SEQRES 3 A 159 PRO GLU VAL VAL ARG GLN ARG ILE VAL ASP LEU ALA HIS SEQRES 4 A 159 GLN GLY VAL ARG PRO CYS ASP ILE SER ARG GLN LEU ARG SEQRES 5 A 159 VAL SER HIS GLY CYS VAL SER LYS ILE LEU GLY ARG TYR SEQRES 6 A 159 TYR GLU THR GLY SER ILE ARG PRO GLY VAL ILE GLY GLY SEQRES 7 A 159 SER LYS PRO LYS VAL ALA THR PRO LYS VAL VAL GLU LYS SEQRES 8 A 159 ILE GLY ASP TYR LYS ARG GLN ASN PRO THR MET PHE ALA SEQRES 9 A 159 TRP GLU ILE ARG ASP ARG LEU LEU ALA GLU GLY VAL CYS SEQRES 10 A 159 ASP ASN ASP THR VAL PRO SER VAL SER SER ILE ASN ARG SEQRES 11 A 159 ILE ILE ARG THR LYS VAL GLN GLN PRO PHE ASN LEU PRO SEQRES 12 A 159 MET ASP SER GLY ALA PRO GLY GLY GLY SER HIS HIS HIS SEQRES 13 A 159 HIS HIS HIS HELIX 1 1 PRO A 27 GLY A 41 1 15 HELIX 2 2 ARG A 43 ARG A 52 1 10 HELIX 3 3 HIS A 55 GLY A 63 1 9 HELIX 4 4 LYS A 87 ASN A 99 1 13 HELIX 5 5 PHE A 103 GLY A 115 1 13 HELIX 6 6 SER A 124 VAL A 136 1 13 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