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- PDB-3mah: A putative c-terminal regulatory domain of aspartate kinase from ... -

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Basic information

Entry
Database: PDB / ID: 3mah
TitleA putative c-terminal regulatory domain of aspartate kinase from porphyromonas gingivalis w83.
ComponentsAspartokinaseAspartate kinase
KeywordsTRANSFERASE / ASPARTATE KINASE / STRUCTURAL GENOMICS / MCSG / PORPHYROMONAS GINGIVALIS / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


aspartate kinase / aspartate kinase activity / threonine biosynthetic process / lysine biosynthetic process via diaminopimelate / ATP binding
Similarity search - Function
Aspartokinase/Bifunctional aspartokinase/homoserine dehydrogenase, catalytic domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / Aspartokinase signature. / ACT domain / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Alpha-Beta Plaits ...Aspartokinase/Bifunctional aspartokinase/homoserine dehydrogenase, catalytic domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / Aspartokinase signature. / ACT domain / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Moy, S. / Joachimiak, A. / Anderson, F.W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: A Putative C-Terminal Regulatory Domain of Aspartate Kinase from Porphyromonas Gingivalis W83.
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Moy, S. / Joachimiak, A. / Anderson, W.F.
History
DepositionMar 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7252
Polymers17,6291
Non-polymers961
Water75742
1
A: Aspartokinase
hetero molecules

A: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4494
Polymers35,2572
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area3880 Å2
ΔGint-32 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.670, 46.670, 221.902
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Aspartokinase / Aspartate kinase


Mass: 17628.645 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: lysC, PG2189, PG_2189 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q7MT13, aspartate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.98 Å3/Da / Density % sol: 37.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris, 1.6 M Ammonium Sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 / Wavelength: 0.97872 Å
DetectorDetector: CCD / Date: Mar 4, 2010 / Details: MIRROR
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→40.42 Å / Num. all: 6972 / Num. obs: 6972 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 15.2 % / Biso Wilson estimate: 52.8 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 63.141
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 16.2 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 18.4 / Rsym value: 0.194 / % possible all: 98.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
ARPWARPmodel building
Cootmodel building
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RESOLVEphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→40.42 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.934 / SU B: 15.643 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.375 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.24 324 4.7 %RANDOM
Rwork0.211 ---
obs0.213 6863 98.24 %-
all-7187 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.48 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å21.05 Å20 Å2
2--2.1 Å20 Å2
3----3.15 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.31→40.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1072 0 5 42 1119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221105
X-RAY DIFFRACTIONr_bond_other_d0.0030.02739
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.9751493
X-RAY DIFFRACTIONr_angle_other_deg0.95431827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1425141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59925.47642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03115210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.945154
X-RAY DIFFRACTIONr_chiral_restr0.1080.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021200
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02203
X-RAY DIFFRACTIONr_mcbond_it0.8371.5700
X-RAY DIFFRACTIONr_mcbond_other0.2081.5286
X-RAY DIFFRACTIONr_mcangle_it1.58121139
X-RAY DIFFRACTIONr_scbond_it2.8113405
X-RAY DIFFRACTIONr_scangle_it4.0654.5354
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 30 -
Rwork0.24 452 -
obs--98.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
114.595918.9126-0.967531.0782-0.65996.16010.0175-0.3132-0.53960.48440.0935-0.3750.52250.2421-0.1110.222-0.00110.01080.1706-0.0080.05518.4145-3.643416.0643
23.5407-0.0471-0.95783.22231.3254.55580.32040.13790.3314-0.1924-0.0869-0.2886-0.73240.5581-0.23350.192-0.09090.05830.1550.01010.100926.4728.96091.897
34.50281.2023-0.68592.4741-0.60426.17670.1079-0.05850.0082-0.08730.01090.34080.0816-0.3325-0.11880.120.0073-0.02180.04360.01050.07944.59771.86278.3374
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A296 - 306
2X-RAY DIFFRACTION2A307 - 375
3X-RAY DIFFRACTION3A376 - 440

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