PDB Short entry for 1NHN HEADER DNA-BINDING 17-NOV-94 1NHN TITLE THE STRUCTURE OF THE HMG BOX AND ITS INTERACTION WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH MOBILITY GROUP PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRICETULUS GRISEUS; SOURCE 3 ORGANISM_COMMON: CHINESE HAMSTER; SOURCE 4 ORGANISM_TAXID: 10029; SOURCE 5 GENE: INSERT DERIVED BY PCR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DH5 ALPHA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PGEX-2T; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-2T GENE: INSERT DERIVED BY PCR KEYWDS DNA-BINDING EXPDTA SOLUTION NMR NUMMDL 41 AUTHOR C.M.READ,P.D.CARY,C.CRANE-ROBINSON,P.C.DRISCOLL,M.O.M.CARILLO, AUTHOR 2 D.G.NORMAN REVDAT 3 23-FEB-22 1NHN 1 REMARK REVDAT 2 24-FEB-09 1NHN 1 VERSN REVDAT 1 07-FEB-95 1NHN 0 JRNL AUTH C.M.READ,P.D.CARY,C.CRANE-ROBINSON,P.C.DRISCOLL, JRNL AUTH 2 M.O.M.CARILLO,D.G.NORMAN JRNL TITL THE STRUCTURE OF THE HMG BOX AND ITS INTERACTION WITH DNA JRNL REF NUCLEIC ACIDS MOL.BIOL. V. 9 222 1995 JRNL REFN ISSN 0933-1891 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.M.READ,P.D.CARY,C.CRANE-ROBINSON,P.C.DRISCOLL,D.G.NORMAN REMARK 1 TITL SOLUTION STRUCTURE OF A DNA-BINDING DOMAIN FROM HMG1 REMARK 1 REF NUCLEIC ACIDS RES. V. 21 3427 1993 REMARK 1 REFN ISSN 0305-1048 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : NILGES (YASAP), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NHN 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_1000175290. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 41 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-41 REMARK 465 RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 SER A 2 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 1 TRP A 43 CG - CD1 - NE1 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 TRP A 43 CD1 - NE1 - CE2 ANGL. DEV. = 8.1 DEGREES REMARK 500 1 TRP A 43 NE1 - CE2 - CZ2 ANGL. DEV. = 8.4 DEGREES REMARK 500 1 TRP A 43 NE1 - CE2 - CD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 ASN A 45 N - CA - CB ANGL. DEV. = -11.3 DEGREES REMARK 500 2 TRP A 43 CG - CD1 - NE1 ANGL. DEV. = -6.8 DEGREES REMARK 500 2 TRP A 43 CD1 - NE1 - CE2 ANGL. DEV. = 8.3 DEGREES REMARK 500 2 TRP A 43 NE1 - CE2 - CZ2 ANGL. DEV. = 8.2 DEGREES REMARK 500 2 TRP A 43 NE1 - CE2 - CD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 3 TRP A 43 CG - CD1 - NE1 ANGL. DEV. = -6.2 DEGREES REMARK 500 3 TRP A 43 CD1 - NE1 - CE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 3 TRP A 43 NE1 - CE2 - CZ2 ANGL. DEV. = 6.8 DEGREES REMARK 500 3 TYR A 54 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 3 TYR A 54 CB - CG - CD1 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 TRP A 43 CG - CD1 - NE1 ANGL. DEV. = -6.6 DEGREES REMARK 500 4 TRP A 43 CD1 - NE1 - CE2 ANGL. DEV. = 8.1 DEGREES REMARK 500 4 TRP A 43 NE1 - CE2 - CZ2 ANGL. DEV. = 7.1 DEGREES REMARK 500 5 TRP A 43 CG - CD1 - NE1 ANGL. DEV. = -6.9 DEGREES REMARK 500 5 TRP A 43 CD1 - NE1 - CE2 ANGL. DEV. = 8.4 DEGREES REMARK 500 5 TRP A 43 NE1 - CE2 - CZ2 ANGL. DEV. = 7.4 DEGREES REMARK 500 5 TRP A 43 NE1 - CE2 - CD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 6 TRP A 43 CG - CD1 - NE1 ANGL. DEV. = -6.1 DEGREES REMARK 500 6 TRP A 43 CD1 - NE1 - CE2 ANGL. DEV. = 7.6 DEGREES REMARK 500 6 TRP A 43 NE1 - CE2 - CZ2 ANGL. DEV. = 7.1 DEGREES REMARK 500 6 TYR A 54 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 6 TYR A 54 CB - CG - CD1 ANGL. DEV. = 4.0 DEGREES REMARK 500 7 TRP A 43 CG - CD1 - NE1 ANGL. DEV. = -6.5 DEGREES REMARK 500 7 TRP A 43 CD1 - NE1 - CE2 ANGL. DEV. = 8.3 DEGREES REMARK 500 8 TRP A 43 CG - CD1 - NE1 ANGL. DEV. = -6.7 DEGREES REMARK 500 8 TRP A 43 CD1 - NE1 - CE2 ANGL. DEV. = 8.2 DEGREES REMARK 500 8 TRP A 43 NE1 - CE2 - CZ2 ANGL. DEV. = 7.3 DEGREES REMARK 500 8 TRP A 43 NE1 - CE2 - CD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 8 TYR A 65 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 8 TYR A 65 CB - CG - CD1 ANGL. DEV. = 5.2 DEGREES REMARK 500 9 TRP A 43 CG - CD1 - NE1 ANGL. DEV. = -6.8 DEGREES REMARK 500 9 TRP A 43 CD1 - NE1 - CE2 ANGL. DEV. = 8.2 DEGREES REMARK 500 9 TRP A 43 NE1 - CE2 - CZ2 ANGL. DEV. = 6.9 DEGREES REMARK 500 10 TRP A 43 CG - CD1 - NE1 ANGL. DEV. = -6.4 DEGREES REMARK 500 10 TRP A 43 CD1 - NE1 - CE2 ANGL. DEV. = 8.0 DEGREES REMARK 500 10 TRP A 43 NE1 - CE2 - CZ2 ANGL. DEV. = 8.0 DEGREES REMARK 500 10 TRP A 43 NE1 - CE2 - CD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 11 TRP A 43 CG - CD1 - NE1 ANGL. DEV. = -6.6 DEGREES REMARK 500 11 TRP A 43 CD1 - NE1 - CE2 ANGL. DEV. = 8.2 DEGREES REMARK 500 11 TRP A 43 NE1 - CE2 - CZ2 ANGL. DEV. = 7.9 DEGREES REMARK 500 11 TRP A 43 NE1 - CE2 - CD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 12 TRP A 43 CG - CD1 - NE1 ANGL. DEV. = -6.9 DEGREES REMARK 500 12 TRP A 43 CD1 - NE1 - CE2 ANGL. DEV. = 8.1 DEGREES REMARK 500 12 TRP A 43 NE1 - CE2 - CZ2 ANGL. DEV. = 8.0 DEGREES REMARK 500 12 TRP A 43 NE1 - CE2 - CD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 12 TYR A 54 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 162 ANGLE DEVIATIONS. 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 ALA A 4 85.16 6.04 REMARK 500 1 PRO A 5 153.64 -35.41 REMARK 500 1 ARG A 7 93.17 1.77 REMARK 500 1 PRO A 9 161.58 -35.99 REMARK 500 1 ALA A 11 -49.27 93.09 REMARK 500 1 HIS A 27 57.15 -110.09 REMARK 500 1 PRO A 28 34.01 -80.52 REMARK 500 1 ASN A 45 45.39 -97.65 REMARK 500 1 THR A 46 -153.88 -96.11 REMARK 500 1 TYR A 65 -70.21 -44.77 REMARK 500 1 ALA A 74 -36.83 -36.21 REMARK 500 1 ASP A 79 41.23 28.39 REMARK 500 1 ALA A 80 41.40 -145.37 REMARK 500 2 ALA A 4 75.63 4.79 REMARK 500 2 PRO A 5 152.94 -37.05 REMARK 500 2 ARG A 7 91.86 -1.87 REMARK 500 2 PRO A 8 -176.56 -67.44 REMARK 500 2 PRO A 9 155.27 -31.85 REMARK 500 2 ALA A 11 -48.63 91.49 REMARK 500 2 HIS A 27 66.44 -115.51 REMARK 500 2 PRO A 28 36.00 -81.95 REMARK 500 2 ASN A 45 39.34 -92.36 REMARK 500 2 THR A 46 -156.31 -105.51 REMARK 500 2 ALA A 74 -9.01 -52.54 REMARK 500 2 ASP A 79 84.15 26.43 REMARK 500 3 ALA A 4 77.32 -1.66 REMARK 500 3 PRO A 5 151.04 -36.39 REMARK 500 3 ARG A 7 87.24 12.00 REMARK 500 3 PRO A 8 -175.66 -68.60 REMARK 500 3 PRO A 9 147.76 -32.47 REMARK 500 3 ALA A 11 -47.33 88.48 REMARK 500 3 HIS A 27 56.95 -116.05 REMARK 500 3 PRO A 28 32.18 -81.94 REMARK 500 3 ASN A 45 38.98 -98.30 REMARK 500 3 THR A 46 -134.89 -85.70 REMARK 500 3 ALA A 48 27.73 26.79 REMARK 500 3 ASP A 49 -21.05 -141.84 REMARK 500 3 LYS A 75 -76.38 -146.72 REMARK 500 3 LYS A 77 -57.98 -141.56 REMARK 500 3 ASP A 79 56.57 22.57 REMARK 500 3 ALA A 80 71.90 -7.78 REMARK 500 4 ALA A 4 67.42 11.65 REMARK 500 4 PRO A 5 154.34 -47.70 REMARK 500 4 ARG A 7 76.45 33.70 REMARK 500 4 PRO A 8 -175.79 -65.18 REMARK 500 4 PRO A 9 157.65 -38.09 REMARK 500 4 ALA A 11 -51.09 93.13 REMARK 500 4 ARG A 20 -60.25 -29.50 REMARK 500 4 HIS A 27 62.61 -117.15 REMARK 500 4 PRO A 28 33.99 -80.91 REMARK 500 REMARK 500 THIS ENTRY HAS 565 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 7 0.18 SIDE CHAIN REMARK 500 1 ARG A 20 0.28 SIDE CHAIN REMARK 500 1 ARG A 73 0.30 SIDE CHAIN REMARK 500 2 ARG A 7 0.31 SIDE CHAIN REMARK 500 2 ARG A 20 0.29 SIDE CHAIN REMARK 500 2 ARG A 73 0.31 SIDE CHAIN REMARK 500 3 ARG A 7 0.31 SIDE CHAIN REMARK 500 3 ARG A 20 0.30 SIDE CHAIN REMARK 500 3 ARG A 73 0.31 SIDE CHAIN REMARK 500 4 ARG A 7 0.30 SIDE CHAIN REMARK 500 4 ARG A 20 0.29 SIDE CHAIN REMARK 500 4 ARG A 73 0.27 SIDE CHAIN REMARK 500 5 ARG A 7 0.32 SIDE CHAIN REMARK 500 5 ARG A 20 0.32 SIDE CHAIN REMARK 500 5 ARG A 73 0.10 SIDE CHAIN REMARK 500 6 ARG A 7 0.31 SIDE CHAIN REMARK 500 6 ARG A 20 0.30 SIDE CHAIN REMARK 500 6 ARG A 73 0.30 SIDE CHAIN REMARK 500 7 ARG A 7 0.29 SIDE CHAIN REMARK 500 7 ARG A 20 0.08 SIDE CHAIN REMARK 500 7 ARG A 73 0.23 SIDE CHAIN REMARK 500 8 ARG A 7 0.28 SIDE CHAIN REMARK 500 8 ARG A 20 0.32 SIDE CHAIN REMARK 500 8 ARG A 73 0.32 SIDE CHAIN REMARK 500 9 ARG A 7 0.30 SIDE CHAIN REMARK 500 9 ARG A 20 0.30 SIDE CHAIN REMARK 500 9 ARG A 73 0.31 SIDE CHAIN REMARK 500 10 ARG A 7 0.32 SIDE CHAIN REMARK 500 10 ARG A 20 0.29 SIDE CHAIN REMARK 500 10 ARG A 73 0.24 SIDE CHAIN REMARK 500 11 ARG A 7 0.26 SIDE CHAIN REMARK 500 11 ARG A 20 0.30 SIDE CHAIN REMARK 500 11 ARG A 73 0.28 SIDE CHAIN REMARK 500 12 ARG A 7 0.26 SIDE CHAIN REMARK 500 12 ARG A 20 0.29 SIDE CHAIN REMARK 500 12 ARG A 73 0.30 SIDE CHAIN REMARK 500 13 ARG A 7 0.28 SIDE CHAIN REMARK 500 13 ARG A 20 0.30 SIDE CHAIN REMARK 500 13 ARG A 73 0.29 SIDE CHAIN REMARK 500 14 ARG A 7 0.27 SIDE CHAIN REMARK 500 14 ARG A 20 0.31 SIDE CHAIN REMARK 500 14 ARG A 73 0.28 SIDE CHAIN REMARK 500 15 ARG A 7 0.28 SIDE CHAIN REMARK 500 15 ARG A 20 0.30 SIDE CHAIN REMARK 500 15 ARG A 73 0.19 SIDE CHAIN REMARK 500 16 ARG A 7 0.31 SIDE CHAIN REMARK 500 16 ARG A 20 0.28 SIDE CHAIN REMARK 500 16 ARG A 73 0.31 SIDE CHAIN REMARK 500 17 ARG A 7 0.23 SIDE CHAIN REMARK 500 17 ARG A 20 0.30 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 121 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NHM RELATED DB: PDB DBREF 1NHN A 3 81 UNP P07156 HMG1_CRIGR 58 136 SEQRES 1 A 81 GLY SER ASN ALA PRO LYS ARG PRO PRO SER ALA PHE PHE SEQRES 2 A 81 LEU PHE CYS SER GLU TYR ARG PRO LYS ILE LYS GLY GLU SEQRES 3 A 81 HIS PRO GLY LEU SER ILE GLY ASP VAL ALA LYS LYS LEU SEQRES 4 A 81 GLY GLU MET TRP ASN ASN THR ALA ALA ASP ASP LYS GLN SEQRES 5 A 81 PRO TYR GLU LYS LYS ALA ALA LYS LEU LYS GLU LYS TYR SEQRES 6 A 81 GLU LYS ASP ILE ALA ALA TYR ARG ALA LYS GLY LYS PRO SEQRES 7 A 81 ASP ALA ALA HELIX 1 H1 PHE A 12 GLU A 18 1 7 HELIX 2 H1' PRO A 21 GLU A 26 1H1 AND H1' BEND AROUND H2 6 HELIX 3 H2 GLY A 33 ASN A 44 1 12 HELIX 4 H3 PRO A 53 ARG A 73 1 21 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