PDB Short entry for 1X2L HEADER TRANSCRIPTION 26-APR-05 1X2L TITLE SOLUTION STRUCTURE OF THE CUT DOMAIN OF HUMAN HOMEOBOX PROTEIN CUX-2 TITLE 2 (CUT-LIKE 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMEOBOX PROTEIN CUX-2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CUT DOMAIN; COMPND 5 SYNONYM: CUT-LIKE 2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CUTL2; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P040531-01; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS CUT DOMAIN, HUMAN HOMEOBOX PROTEIN CUX-2, CUT-LIKE 2, STRUCTURAL KEYWDS 2 GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND KEYWDS 3 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.O.KAMATARI,T.TOMIZAWA,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 02-MAR-22 1X2L 1 REMARK SEQADV REVDAT 2 24-FEB-09 1X2L 1 VERSN REVDAT 1 26-OCT-05 1X2L 0 JRNL AUTH Y.O.KAMATARI,T.TOMIZAWA,S.KOSHIBA,M.INOUE,T.KIGAWA, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE CUT DOMAIN OF HUMAN HOMEOBOX JRNL TITL 2 PROTEIN CUX-2 (CUT-LIKE 2) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, OPALP 1.2 REMARK 3 AUTHORS : BRUKER (XWINNMR), KORADI, R., BILLETER, M., REMARK 3 GUNTERT, P. (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1X2L COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000024299. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.19MM CUT DOMAIN U-13C, 15N; REMARK 210 20MM D-TRIS-HCL BUFFER (PH7.0); REMARK 210 100MM NACL; 1MM D-DTT; 0.02% 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 : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9295, CYANA 1.07 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION,STRUCTURES WITH REMARK 210 THE LEAST RESTRAINT VIOLATIONS 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: 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 3 VAL A 52 CA - CB - CG2 ANGL. DEV. = 9.2 DEGREES REMARK 500 11 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 LEU A 87 CB - CG - CD1 ANGL. DEV. = 10.9 DEGREES REMARK 500 17 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.3 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 SER A 2 111.12 65.50 REMARK 500 1 SER A 3 -88.25 -131.80 REMARK 500 1 ARG A 95 30.41 -77.11 REMARK 500 1 SER A 100 171.07 63.90 REMARK 500 2 SER A 2 175.29 67.06 REMARK 500 2 SER A 6 -175.33 59.25 REMARK 500 2 ALA A 8 8.19 55.83 REMARK 500 2 PRO A 10 -159.71 -72.49 REMARK 500 2 GLU A 13 -155.09 48.81 REMARK 500 2 ASN A 34 71.22 50.74 REMARK 500 2 TYR A 43 -67.93 -96.22 REMARK 500 2 ASP A 82 118.55 -160.03 REMARK 500 2 SER A 99 -167.42 62.11 REMARK 500 3 GLU A 13 -151.57 50.70 REMARK 500 3 GLU A 15 -147.61 -127.40 REMARK 500 3 TYR A 43 -72.57 -103.15 REMARK 500 3 ARG A 95 33.04 -83.27 REMARK 500 3 PRO A 98 99.79 -69.69 REMARK 500 3 SER A 100 80.33 57.38 REMARK 500 4 SER A 2 -179.15 58.75 REMARK 500 4 SER A 3 2.78 53.69 REMARK 500 4 ALA A 12 -105.41 56.20 REMARK 500 4 GLU A 13 -166.97 -125.28 REMARK 500 4 ASP A 18 98.38 -69.75 REMARK 500 4 ASN A 34 75.59 39.75 REMARK 500 4 TYR A 43 -78.73 -106.63 REMARK 500 4 PRO A 98 46.99 -77.43 REMARK 500 5 SER A 2 108.26 174.69 REMARK 500 5 ALA A 8 168.14 66.82 REMARK 500 5 ASN A 34 71.76 46.62 REMARK 500 5 TYR A 43 -76.98 -96.73 REMARK 500 5 SER A 100 109.44 68.44 REMARK 500 6 SER A 2 -70.10 -174.51 REMARK 500 6 SER A 6 157.97 69.37 REMARK 500 6 PRO A 10 -175.08 -67.59 REMARK 500 6 GLU A 13 -172.57 57.77 REMARK 500 6 ASN A 34 72.73 42.33 REMARK 500 6 TYR A 43 -61.10 -121.99 REMARK 500 6 PRO A 59 98.91 -68.41 REMARK 500 6 SER A 100 -88.28 -145.78 REMARK 500 7 SER A 5 82.73 -152.11 REMARK 500 7 GLN A 37 -35.99 -39.62 REMARK 500 7 ARG A 95 27.06 -76.78 REMARK 500 7 SER A 99 11.60 -69.69 REMARK 500 8 ALA A 12 148.27 59.75 REMARK 500 8 ASN A 34 54.31 38.40 REMARK 500 8 SER A 96 155.29 -48.39 REMARK 500 9 SER A 3 174.65 54.48 REMARK 500 9 ASN A 34 85.11 41.01 REMARK 500 9 TYR A 43 -78.50 -96.31 REMARK 500 REMARK 500 THIS ENTRY HAS 125 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 GLU A 13 GLU A 14 1 147.75 REMARK 500 GLY A 1 SER A 2 5 -140.52 REMARK 500 GLY A 1 SER A 2 8 144.92 REMARK 500 SER A 5 SER A 6 15 -144.14 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 ARG A 90 0.09 SIDE CHAIN REMARK 500 3 ARG A 90 0.09 SIDE CHAIN REMARK 500 5 ARG A 38 0.11 SIDE CHAIN REMARK 500 5 ARG A 63 0.13 SIDE CHAIN REMARK 500 5 ARG A 95 0.09 SIDE CHAIN REMARK 500 7 ARG A 90 0.08 SIDE CHAIN REMARK 500 11 PHE A 24 0.08 SIDE CHAIN REMARK 500 11 ARG A 90 0.10 SIDE CHAIN REMARK 500 12 ARG A 95 0.10 SIDE CHAIN REMARK 500 13 ARG A 38 0.10 SIDE CHAIN REMARK 500 17 ARG A 95 0.08 SIDE CHAIN REMARK 500 19 ARG A 90 0.09 SIDE CHAIN REMARK 500 19 ARG A 95 0.08 SIDE CHAIN REMARK 500 20 ARG A 90 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSK002100285.3 RELATED DB: TARGETDB DBREF 1X2L A 8 95 UNP O14529 CUTL2_HUMAN 563 650 SEQADV 1X2L GLY A 1 UNP O14529 CLONING ARTIFACT SEQADV 1X2L SER A 2 UNP O14529 CLONING ARTIFACT SEQADV 1X2L SER A 3 UNP O14529 CLONING ARTIFACT SEQADV 1X2L GLY A 4 UNP O14529 CLONING ARTIFACT SEQADV 1X2L SER A 5 UNP O14529 CLONING ARTIFACT SEQADV 1X2L SER A 6 UNP O14529 CLONING ARTIFACT SEQADV 1X2L GLY A 7 UNP O14529 CLONING ARTIFACT SEQADV 1X2L SER A 96 UNP O14529 CLONING ARTIFACT SEQADV 1X2L GLY A 97 UNP O14529 CLONING ARTIFACT SEQADV 1X2L PRO A 98 UNP O14529 CLONING ARTIFACT SEQADV 1X2L SER A 99 UNP O14529 CLONING ARTIFACT SEQADV 1X2L SER A 100 UNP O14529 CLONING ARTIFACT SEQADV 1X2L GLY A 101 UNP O14529 CLONING ARTIFACT SEQRES 1 A 101 GLY SER SER GLY SER SER GLY ALA GLY PRO GLY ALA GLU SEQRES 2 A 101 GLU GLU GLN LEU ASP THR ALA GLU ILE ALA PHE GLN VAL SEQRES 3 A 101 LYS GLU GLN LEU LEU LYS HIS ASN ILE GLY GLN ARG VAL SEQRES 4 A 101 PHE GLY HIS TYR VAL LEU GLY LEU SER GLN GLY SER VAL SEQRES 5 A 101 SER GLU ILE LEU ALA ARG PRO LYS PRO TRP ARG LYS LEU SEQRES 6 A 101 THR VAL LYS GLY LYS GLU PRO PHE ILE LYS MET LYS GLN SEQRES 7 A 101 PHE LEU SER ASP GLU GLN ASN VAL LEU ALA LEU ARG THR SEQRES 8 A 101 ILE GLN VAL ARG SER GLY PRO SER SER GLY HELIX 1 1 ASP A 18 HIS A 33 1 16 HELIX 2 2 GLY A 36 VAL A 44 1 9 HELIX 3 3 SER A 48 ARG A 58 1 11 HELIX 4 4 PRO A 61 LEU A 65 5 5 HELIX 5 5 THR A 66 SER A 81 1 16 HELIX 6 6 GLU A 83 ARG A 95 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