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- PDB-2czl: Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic ... -

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Basic information

Entry
Database: PDB / ID: 2czl
TitleCrystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8 (Cys11 modified with beta-mercaptoethanol)
Componentshypothetical protein TTHA1568Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved hypothetical protein / TTHA1568 / Extremely thermophilic bacteria / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases / carbon-carbon lyase activity / menaquinone biosynthetic process
Similarity search - Function
1,4-dihydroxy-6-naphtoate synthase / Menaquinone biosynthesis enzyme / Menaquinone biosynthesis / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / L(+)-TARTARIC ACID / : / 1,4-dihydroxy-6-naphtoate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsArai, R. / Nishino, A. / Nagano, K. / Kamo-Uchikubo, T. / Nishimoto, M. / Toyama, M. / Terada, T. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Struct.Biol. / Year: 2009
Title: Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8.
Authors: Arai, R. / Murayama, K. / Uchikubo-Kamo, T. / Nishimoto, M. / Toyama, M. / Kuramitsu, S. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionJul 13, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein TTHA1568
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7924
Polymers30,1451
Non-polymers6483
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.236, 60.236, 171.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-905-

HOH

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Components

#1: Protein hypothetical protein TTHA1568 / Hypothesis


Mass: 30144.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1568 / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 55981537, UniProt: Q5SI12*PLUS
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL / Polyethylene glycol


Mass: 458.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6453.3
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop7.50.1M Tris-HCl, 0.8M Potassium sodium tartrate, 2.5% PEG 5000, MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop80.1M Tris-HCl, 0.8M Potassium sodium tartrate, 0.75% PEG 5000, MME, 5mM K2PtCl4, 16h soaking, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B121.07181, 1.07216, 1.05000
Detector
TypeIDDetectorDateDetails
RIGAKU JUPITER 2101CCDApr 16, 2005Two dimensional focusing mirror
RIGAKU JUPITER 2102CCDMay 25, 2005Two dimensional focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si double crystalSINGLE WAVELENGTHMx-ray1
2Si double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.071811
31.072161
41.051
ReflectionResolution: 1.55→50 Å / Num. obs: 45583 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.071 / Net I/σ(I): 18.79
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 5.05 / Num. unique all: 4258 / Rsym value: 0.282 / % possible all: 93.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→42.82 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 670101.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.209 4520 10.1 %RANDOM
Rwork0.182 ---
obs-44576 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.8724 Å2 / ksol: 0.368804 e/Å3
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.55→42.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 42 316 2471
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.341.5
X-RAY DIFFRACTIONc_mcangle_it2.962
X-RAY DIFFRACTIONc_scbond_it3.542
X-RAY DIFFRACTIONc_scangle_it4.752.5
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 649 9.6 %
Rwork0.213 6096 -
obs-6745 88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_CME.paramprotein_CME.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4tla.paramtla.top
X-RAY DIFFRACTION5pegf_7.parampegf_7.top

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