HEADER TRANSCRIPTION 09-JAN-13 2M34
TITLE NMR STRUCTURE OF THE HOMEODOMAIN TRANSCRIPTION FACTOR GBX1 FROM HOMO
TITLE 2 SAPIENS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HOMEOBOX PROTEIN GBX-1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: DNA BINDING HOMEOBOX RESIDUES 256-325;
COMPND 5 SYNONYM: GASTRULATION AND BRAIN-SPECIFIC HOMEOBOX PROTEIN 1;
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: GBX1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET46
KEYWDS HOMEODOMAIN, DNA BINDING, TRANSCRIPTION, STRUCTURAL GENOMICS, PSI-
KEYWDS 2 BIOLOGY, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PARTNERSHIP FOR
KEYWDS 3 STEM CELL BIOLOGY, STEMCELL
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR A.PROUDFOOT,P.SERRANO,M.GERALT,K.WUTHRICH,PARTNERSHIP FOR STEM CELL
AUTHOR 2 BIOLOGY (STEMCELL),JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG)
REVDAT 3 14-JUN-23 2M34 1 REMARK SEQADV
REVDAT 2 30-JAN-13 2M34 1 AUTHOR
REVDAT 1 23-JAN-13 2M34 0
JRNL AUTH A.PROUDFOOT,K.WUTHRICH
JRNL TITL NMR STRUCTURE OF THE HOMEODOMAIN TRANSCRIPTION FACTOR GBX1
JRNL TITL 2 FROM HOMO SAPIENS
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CYANA, OPALP
REMARK 3 AUTHORS : GUNTERT P. (CYANA), LUGINBUHL, GUNTERT, BILLETER
REMARK 3 AND WUTHRICH (OPALP)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2M34 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-13.
REMARK 100 THE DEPOSITION ID IS D_1000103148.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.5
REMARK 210 IONIC STRENGTH : 0.220
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-98% 13C; U-98% 15N]
REMARK 210 PROTEIN, 50 MM SODIUM CHLORIDE,
REMARK 210 20 MM SODIUM PHOSPHATE, 5 MM
REMARK 210 SODIUM AZIDE, 95% H2O/5% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-13C NOESY
REMARK 210 ALIPHATIC; 3D 1H-13C NOESY
REMARK 210 AROMATIC; 3D 1H-15N NOESY; APSY
REMARK 210 4D-HACANH; APSY 5D-CBCACONH;
REMARK 210 APSY 5D-HACACONH
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : TOPSPIN, UNIO, CARA
REMARK 210 METHOD USED : MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 80
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION
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 ARG A 9 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES
REMARK 500 12 HIS A 42 CB - CG - CD2 ANGL. DEV. = -10.4 DEGREES
REMARK 500 13 ARG A 11 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500 16 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 16 ARG A 37 NE - CZ - NH2 ANGL. DEV. = -3.7 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 ARG A 8 -161.04 63.16
REMARK 500 1 ARG A 9 -61.12 76.61
REMARK 500 1 ARG A 10 20.46 45.17
REMARK 500 1 ARG A 11 14.11 -141.39
REMARK 500 1 THR A 12 -166.07 -125.34
REMARK 500 1 CYS A 28 -63.34 -90.04
REMARK 500 1 LYS A 45 25.97 47.58
REMARK 500 2 ALA A 2 85.37 -150.01
REMARK 500 2 PRO A 3 -169.74 -76.85
REMARK 500 2 LYS A 6 -176.59 55.14
REMARK 500 2 ARG A 9 -64.86 -153.33
REMARK 500 2 THR A 12 -173.75 53.28
REMARK 500 2 CYS A 28 -63.29 -103.91
REMARK 500 2 ASN A 69 14.29 -143.01
REMARK 500 3 ALA A 2 79.50 -156.74
REMARK 500 3 ARG A 8 35.45 -152.52
REMARK 500 3 ARG A 10 57.34 -67.71
REMARK 500 3 THR A 12 115.37 64.20
REMARK 500 3 ALA A 13 -84.13 44.59
REMARK 500 3 CYS A 28 -70.82 -78.13
REMARK 500 3 LYS A 30 -34.38 -132.27
REMARK 500 3 ILE A 65 -50.43 -123.80
REMARK 500 4 ALA A 2 85.21 -155.87
REMARK 500 4 THR A 12 -175.14 52.70
REMARK 500 4 CYS A 28 -51.99 -127.33
REMARK 500 4 ALA A 67 50.35 174.72
REMARK 500 5 SER A 7 -62.61 -142.22
REMARK 500 5 ARG A 9 -55.02 -143.48
REMARK 500 5 THR A 12 160.73 67.75
REMARK 500 6 SER A 7 -46.07 -159.15
REMARK 500 6 ARG A 10 84.44 -60.06
REMARK 500 6 ARG A 11 15.92 -166.91
REMARK 500 6 THR A 12 -169.77 -162.90
REMARK 500 6 HIS A 27 -70.37 -67.45
REMARK 500 6 ASN A 69 74.01 42.65
REMARK 500 7 LYS A 6 6.41 -69.01
REMARK 500 7 SER A 7 -85.16 62.64
REMARK 500 7 ARG A 10 32.93 -62.02
REMARK 500 7 ALA A 13 -77.73 55.14
REMARK 500 7 THR A 15 -164.50 -106.54
REMARK 500 7 GLN A 18 2.01 -69.93
REMARK 500 7 LEU A 46 -169.83 -121.51
REMARK 500 8 ARG A 10 65.02 -58.77
REMARK 500 8 ARG A 11 16.71 -154.08
REMARK 500 8 ALA A 43 -75.35 -55.65
REMARK 500 8 LYS A 45 73.52 62.45
REMARK 500 8 ALA A 67 -29.39 59.64
REMARK 500 9 ARG A 10 23.95 49.27
REMARK 500 9 THR A 12 109.18 70.03
REMARK 500 9 ALA A 13 -62.57 61.31
REMARK 500
REMARK 500 THIS ENTRY HAS 118 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 VAL A 70 SER A 71 6 -138.78
REMARK 500 VAL A 70 SER A 71 8 149.34
REMARK 500 VAL A 70 SER A 71 10 -145.84
REMARK 500 VAL A 70 SER A 71 17 144.47
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 8 0.08 SIDE CHAIN
REMARK 500 6 ARG A 8 0.10 SIDE CHAIN
REMARK 500 6 ARG A 59 0.13 SIDE CHAIN
REMARK 500 7 ARG A 64 0.08 SIDE CHAIN
REMARK 500 8 ARG A 59 0.08 SIDE CHAIN
REMARK 500 12 HIS A 42 0.07 SIDE CHAIN
REMARK 500 12 ARG A 58 0.09 SIDE CHAIN
REMARK 500 13 ARG A 59 0.09 SIDE CHAIN
REMARK 500 15 ARG A 59 0.08 SIDE CHAIN
REMARK 500 17 TYR A 31 0.07 SIDE CHAIN
REMARK 500 18 ARG A 64 0.09 SIDE CHAIN
REMARK 500 19 ARG A 8 0.10 SIDE CHAIN
REMARK 500 19 ARG A 58 0.09 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 18944 RELATED DB: BMRB
REMARK 900 RELATED ID: JCSG-424577 RELATED DB: TARGETTRACK
DBREF 2M34 A 2 71 UNP Q14549 GBX1_HUMAN 256 325
SEQADV 2M34 SER A 1 UNP Q14549 EXPRESSION TAG
SEQRES 1 A 71 SER ALA PRO GLY GLY LYS SER ARG ARG ARG ARG THR ALA
SEQRES 2 A 71 PHE THR SER GLU GLN LEU LEU GLU LEU GLU LYS GLU PHE
SEQRES 3 A 71 HIS CYS LYS LYS TYR LEU SER LEU THR GLU ARG SER GLN
SEQRES 4 A 71 ILE ALA HIS ALA LEU LYS LEU SER GLU VAL GLN VAL LYS
SEQRES 5 A 71 ILE TRP PHE GLN ASN ARG ARG ALA LYS TRP LYS ARG ILE
SEQRES 6 A 71 LYS ALA GLY ASN VAL SER
HELIX 1 1 THR A 15 LYS A 29 1 15
HELIX 2 2 SER A 33 LEU A 44 1 12
HELIX 3 3 SER A 47 ALA A 67 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
MODEL 1
(ATOM LINES ARE NOT SHOWN.)
END
