HEADER DNA BINDING PROTEIN 23-JAN-03 1J3D TITLE SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF THE HMGB2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH MOBILITY GROUP PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, B DOMAIN; COMPND 5 SYNONYM: HIGH MOBILITY GROUP B2, HMG2, HMGB2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_COMMON: PIG; SOURCE 4 ORGANISM_TAXID: 9823; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: PET; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-22B KEYWDS HMG-BOX, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR J.KURITA,H.SHIMAHARA,M.YOSHIDA,S.TATE REVDAT 4 27-DEC-23 1J3D 1 REMARK REVDAT 3 23-FEB-22 1J3D 1 REMARK SEQADV REVDAT 2 24-FEB-09 1J3D 1 VERSN REVDAT 1 25-MAY-04 1J3D 0 JRNL AUTH J.KURITA,H.SHIMAHARA,M.YOSHIDA,S.TATE JRNL TITL STRUCUTRAL COMPARISON OF TWO HMG-BOXES IN THE NON-HISTONE JRNL TITL 2 PROTEIN HMG-2 WITH IN THE HMG-1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.1, X-PLOR 3.851 REMARK 3 AUTHORS : NILGES (ARIA), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1J3D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1000005579. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 303 REMARK 210 PH : 5.0; 6.4 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM C-TERMINAL DOMAIN U-15N,13C; REMARK 210 50MM ACETATE BUFFER NA; 1MM C- REMARK 210 TERMINAL DOMAIN NON-LABEL; 50MM REMARK 210 ACETATE BUFFER NA; 1MM C- REMARK 210 TERMINAL DOMAIN U-15N; 50MM REMARK 210 PHOSPHATE BUFFER NA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D NOESY; CT_ REMARK 210 HMQC; IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2001.157.17.50 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 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: THE 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: 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 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 LEU A 17 -73.80 -64.99 REMARK 500 1 HIS A 30 83.87 -152.57 REMARK 500 1 LEU A 33 102.62 -50.35 REMARK 500 1 SER A 34 -171.48 -56.89 REMARK 500 1 SER A 50 -146.37 -93.81 REMARK 500 1 LYS A 54 -34.20 -172.61 REMARK 500 1 ALA A 77 59.36 -161.56 REMARK 500 2 PRO A 12 -165.38 -71.70 REMARK 500 2 SER A 13 44.72 -167.81 REMARK 500 2 ALA A 14 -72.01 71.21 REMARK 500 2 LEU A 17 -76.11 -63.61 REMARK 500 2 HIS A 30 82.44 -150.16 REMARK 500 2 LEU A 33 108.73 -48.72 REMARK 500 2 SER A 34 -167.06 -73.44 REMARK 500 2 SER A 50 -118.36 -93.75 REMARK 500 2 ASP A 53 57.98 -119.82 REMARK 500 2 LYS A 54 -31.02 -170.13 REMARK 500 3 LYS A 9 -175.76 -56.25 REMARK 500 3 PRO A 12 -167.69 -71.00 REMARK 500 3 SER A 13 45.07 -168.91 REMARK 500 3 ALA A 14 -69.71 73.26 REMARK 500 3 LEU A 17 -71.84 -65.70 REMARK 500 3 HIS A 30 75.64 -154.77 REMARK 500 3 LEU A 33 100.34 -51.56 REMARK 500 3 SER A 34 -171.10 -57.08 REMARK 500 3 SER A 50 -110.26 -95.98 REMARK 500 3 LYS A 54 -32.71 -170.43 REMARK 500 4 PRO A 12 -163.91 -69.72 REMARK 500 4 SER A 13 50.46 -174.09 REMARK 500 4 ALA A 14 -69.69 73.33 REMARK 500 4 LEU A 17 -72.68 -66.27 REMARK 500 4 SER A 34 -168.87 -105.02 REMARK 500 4 ASP A 37 -54.79 -147.23 REMARK 500 4 SER A 50 -149.68 -91.83 REMARK 500 4 ASP A 53 54.89 -119.36 REMARK 500 4 LYS A 54 -33.01 -168.43 REMARK 500 5 SER A 13 39.89 -162.50 REMARK 500 5 ALA A 14 -73.27 70.08 REMARK 500 5 LEU A 17 -71.14 -66.56 REMARK 500 5 SER A 34 -168.86 -105.02 REMARK 500 5 ASP A 37 -52.77 -148.69 REMARK 500 5 SER A 50 -149.83 -90.45 REMARK 500 5 LYS A 54 -35.28 -171.29 REMARK 500 5 GLN A 59 -70.20 -77.55 REMARK 500 5 ALA A 77 98.39 -176.59 REMARK 500 6 SER A 13 39.09 -161.53 REMARK 500 6 ALA A 14 -72.75 70.61 REMARK 500 6 LEU A 17 -70.12 -67.86 REMARK 500 6 HIS A 30 80.81 -151.59 REMARK 500 6 SER A 34 -164.34 -59.46 REMARK 500 REMARK 500 THIS ENTRY HAS 275 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 10 0.31 SIDE CHAIN REMARK 500 1 ARG A 23 0.27 SIDE CHAIN REMARK 500 1 ARG A 76 0.28 SIDE CHAIN REMARK 500 2 ARG A 10 0.32 SIDE CHAIN REMARK 500 2 ARG A 23 0.29 SIDE CHAIN REMARK 500 2 ARG A 76 0.25 SIDE CHAIN REMARK 500 3 ARG A 10 0.27 SIDE CHAIN REMARK 500 3 ARG A 23 0.32 SIDE CHAIN REMARK 500 3 ARG A 76 0.32 SIDE CHAIN REMARK 500 4 ARG A 10 0.28 SIDE CHAIN REMARK 500 4 ARG A 23 0.30 SIDE CHAIN REMARK 500 4 ARG A 76 0.30 SIDE CHAIN REMARK 500 5 ARG A 10 0.31 SIDE CHAIN REMARK 500 5 ARG A 23 0.29 SIDE CHAIN REMARK 500 5 ARG A 76 0.31 SIDE CHAIN REMARK 500 6 ARG A 10 0.31 SIDE CHAIN REMARK 500 6 ARG A 23 0.29 SIDE CHAIN REMARK 500 6 ARG A 76 0.29 SIDE CHAIN REMARK 500 7 ARG A 10 0.30 SIDE CHAIN REMARK 500 7 ARG A 23 0.25 SIDE CHAIN REMARK 500 7 ARG A 76 0.25 SIDE CHAIN REMARK 500 8 ARG A 10 0.27 SIDE CHAIN REMARK 500 8 ARG A 23 0.32 SIDE CHAIN REMARK 500 8 ARG A 76 0.29 SIDE CHAIN REMARK 500 9 ARG A 10 0.32 SIDE CHAIN REMARK 500 9 ARG A 23 0.22 SIDE CHAIN REMARK 500 9 ARG A 76 0.27 SIDE CHAIN REMARK 500 10 ARG A 10 0.30 SIDE CHAIN REMARK 500 10 ARG A 23 0.28 SIDE CHAIN REMARK 500 10 ARG A 76 0.31 SIDE CHAIN REMARK 500 11 ARG A 10 0.31 SIDE CHAIN REMARK 500 11 ARG A 23 0.31 SIDE CHAIN REMARK 500 11 ARG A 76 0.31 SIDE CHAIN REMARK 500 12 ARG A 10 0.31 SIDE CHAIN REMARK 500 12 ARG A 23 0.29 SIDE CHAIN REMARK 500 12 ARG A 76 0.29 SIDE CHAIN REMARK 500 13 ARG A 10 0.27 SIDE CHAIN REMARK 500 13 ARG A 23 0.29 SIDE CHAIN REMARK 500 13 ARG A 76 0.31 SIDE CHAIN REMARK 500 14 ARG A 10 0.29 SIDE CHAIN REMARK 500 14 ARG A 23 0.31 SIDE CHAIN REMARK 500 14 ARG A 76 0.32 SIDE CHAIN REMARK 500 15 ARG A 10 0.32 SIDE CHAIN REMARK 500 15 ARG A 23 0.30 SIDE CHAIN REMARK 500 15 ARG A 76 0.26 SIDE CHAIN REMARK 500 16 ARG A 10 0.28 SIDE CHAIN REMARK 500 16 ARG A 23 0.28 SIDE CHAIN REMARK 500 16 ARG A 76 0.31 SIDE CHAIN REMARK 500 17 ARG A 10 0.30 SIDE CHAIN REMARK 500 17 ARG A 23 0.27 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 90 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J3C RELATED DB: PDB REMARK 900 THE SAME PROTEIN, H108Y MUTANT DBREF 1J3D A 2 78 UNP P17741 HMG2_PIG 88 164 SEQADV 1J3D MET A 1 UNP P17741 INITIATING METHIONINE SEQRES 1 A 78 MET LYS LYS ASP PRO ASN ALA PRO LYS ARG PRO PRO SER SEQRES 2 A 78 ALA PHE PHE LEU PHE CYS SER GLU HIS ARG PRO LYS ILE SEQRES 3 A 78 LYS SER GLU HIS PRO GLY LEU SER ILE GLY ASP THR ALA SEQRES 4 A 78 LYS LYS LEU GLY GLU MET TRP SER GLU GLN SER ALA LYS SEQRES 5 A 78 ASP LYS GLN PRO TYR GLU GLN LYS ALA ALA LYS LEU LYS SEQRES 6 A 78 GLU LYS TYR GLU LYS ASP ILE ALA ALA TYR ARG ALA LYS HELIX 1 1 SER A 13 LYS A 27 1 15 HELIX 2 2 GLY A 36 SER A 47 1 12 HELIX 3 3 LYS A 54 LYS A 78 1 25 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