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- PDB-3k85: Crystal structure of a D-glycero-D-manno-heptose 1-phosphate kina... -

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Basic information

Entry
Database: PDB / ID: 3k85
TitleCrystal structure of a D-glycero-D-manno-heptose 1-phosphate kinase from Bacteriodes thetaiotaomicron
ComponentsD-glycero-D-manno-heptose 1-phosphate kinase
KeywordsTRANSFERASE / Kinase / Bacteriodes thetaiotaomicron / Protein Structure Initiative II(PSI II) / NYSGXRC / 11277b / Structural Genomics / New York SGX Research Center for Structural Genomics / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


kinase activity / ATP binding
Similarity search - Function
Ribosomal Protein S5; domain 2 - #120 / D,D-heptose 7-phosphate kinase / Galactokinase/homoserine kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold ...Ribosomal Protein S5; domain 2 - #120 / D,D-heptose 7-phosphate kinase / Galactokinase/homoserine kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D-glycero-D-manno-heptose 1-phosphate kinase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsPalani, K. / Kumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a D-glycero-D-manno-heptose 1-phosphate kinase from Bacteriodes thetaiotaomicron
Authors: Palani, K. / Kumaran, D. / Burley, S.K. / Swaminathan, S.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-glycero-D-manno-heptose 1-phosphate kinase
B: D-glycero-D-manno-heptose 1-phosphate kinase


Theoretical massNumber of molelcules
Total (without water)79,5772
Polymers79,5772
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: D-glycero-D-manno-heptose 1-phosphate kinase
B: D-glycero-D-manno-heptose 1-phosphate kinase

A: D-glycero-D-manno-heptose 1-phosphate kinase
B: D-glycero-D-manno-heptose 1-phosphate kinase


Theoretical massNumber of molelcules
Total (without water)159,1534
Polymers159,1534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area8770 Å2
ΔGint-12 kcal/mol
Surface area49590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.889, 149.469, 141.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein D-glycero-D-manno-heptose 1-phosphate kinase


Mass: 39788.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT-0704, BT_0474 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8AAJ0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 0.2M Ammonium sulfate, 0.1M HEPES, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2009 / Details: MIRRORS
RadiationMonochromator: SI(III) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.28→40.95 Å / Num. obs: 38392 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 24.3 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.9
Reflection shellResolution: 2.28→2.37 Å / Redundancy: 21.6 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2.4 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.28→40.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 98691.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1677 5.1 %RANDOM
Rwork0.254 ---
obs0.254 33035 94.1 %-
all-38392 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.7558 Å2 / ksol: 0.309786 e/Å3
Displacement parametersBiso mean: 43.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.91 Å20 Å20 Å2
2--15.49 Å20 Å2
3----11.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.28→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4742 0 0 137 4879
Refine LS restraints
Refine-IDTypeDev ideal
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_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.28→2.42 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 269 5.5 %
Rwork0.321 4651 -
obs--85.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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