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- PDB-1kq4: CRYSTAL STRUCTURE OF A THY1-COMPLEMENTING PROTEIN (TM0449) FROM T... -

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Basic information

Entry
Database: PDB / ID: 1kq4
TitleCRYSTAL STRUCTURE OF A THY1-COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA AT 2.25 A RESOLUTION
ComponentsHYPOTHETICAL PROTEIN TM0449
KeywordsTRANSFERASE / THY1-COMPLEMENTING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / NADPH binding / flavin adenine dinucleotide binding / methylation
Similarity search - Function
Gyrase A; domain 2 - #170 / Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile. / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsWilson, I.A. / Miller, M.D. / Joint Center for Structural Genomics (JCSG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline
Authors: Lesley, S.A. / Kuhn, P. / Godzik, A. / Deacon, A.M. / Mathews, I. / Kreusch, A. / Spraggon, G. / Klock, H.E. / McMullan, D. / Shin, T. / Vincent, J. / Robb, A. / Brinen, L.S. / Miller, M.D. ...Authors: Lesley, S.A. / Kuhn, P. / Godzik, A. / Deacon, A.M. / Mathews, I. / Kreusch, A. / Spraggon, G. / Klock, H.E. / McMullan, D. / Shin, T. / Vincent, J. / Robb, A. / Brinen, L.S. / Miller, M.D. / McPhillips, T.M. / Miller, M.A. / Scheibe, D. / Canaves, J.M. / Guda, C. / Jaroszewski, L. / Selby, T.L. / Elsliger, M.-A. / Wooley, J. / Taylor, S.S. / Hodgson, K.O. / Wilson, I.A. / Schultz, P.G. / Stevens, R.C.
History
DepositionJan 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN TM0449
B: HYPOTHETICAL PROTEIN TM0449
C: HYPOTHETICAL PROTEIN TM0449
D: HYPOTHETICAL PROTEIN TM0449
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2828
Polymers111,1404
Non-polymers3,1424
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20050 Å2
ΔGint-74 kcal/mol
Surface area32180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.200, 116.610, 141.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homotetramer. The coordinates represent the asymmetric unit.

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Components

#1: Protein
HYPOTHETICAL PROTEIN TM0449


Mass: 27785.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0449 / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9WYT0
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 50% (v/v)PEG-200, 0.1M HEPES pH7.5, final pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 30, 2001
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 43752 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.061 / Net I/σ(I): 10.6
Reflection shellResolution: 2.25→2.27 Å / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Redundancy: 3.4 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
RESOLVEmodel building
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→20 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.24 4409 10 %RANDOM
Rwork0.192 ---
obs0.192 43369 99 %-
all-43450 --
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1--9.296 Å20 Å20 Å2
2--3.164 Å20 Å2
3---6.132 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6981 0 212 274 7467
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3981.5
X-RAY DIFFRACTIONc_mcangle_it2.2282
X-RAY DIFFRACTIONc_scbond_it2.3792
X-RAY DIFFRACTIONc_scangle_it3.512.5
LS refinement shellResolution: 2.25→2.27 Å /
RfactorNum. reflection
Rfree0.24 77
Rwork0.207 -
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2FAD.PAR
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30 Å2

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