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- PDB-6jdo: Crystal structure of N-acetyl mannosmaine kinase with AMP-PNP fro... -

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Basic information

Entry
Database: PDB / ID: 6jdo
TitleCrystal structure of N-acetyl mannosmaine kinase with AMP-PNP from Pasteurella multocida
ComponentsN-acetylmannosamine kinase
KeywordsSUGAR BINDING PROTEIN / Kinase / ManNAc binding protein / two domain protein
Function / homology
Function and homology information


N-acetylmannosamine metabolic process / N-acylmannosamine kinase activity / N-acylmannosamine kinase / N-acetylneuraminate catabolic process / zinc ion binding / ATP binding
Similarity search - Function
N-acetylmannosamine kinase, bacterial / ROK family / ROK family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / N-acetylmannosamine kinase / N-acetylmannosamine kinase
Similarity search - Component
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsThanuja, G. / Ramaswamy, S.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (India)BT/IN/Sweden/06/SR/2017-18 India
Department of Biotechnology (India)BT/PR12422/MED/31/287/ 2014 India
CitationJournal: Acs Omega / Year: 2020
Title: Structure and Function of N‐Acetylmannosamine Kinases from Pathogenic Bacteria.
Authors: Thanuja, G. / Ramaswamy, S.
History
DepositionFeb 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylmannosamine kinase
B: N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8416
Polymers61,7482
Non-polymers1,0934
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-39 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.433, 126.433, 82.912
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-559-

HOH

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Components

#1: Protein N-acetylmannosamine kinase / ManNAc kinase / N-acetyl-D-mannosamine kinase


Mass: 30874.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pasteurella multocida (bacteria) / Gene: nanK / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A2K0XYW4, UniProt: Q9CKB3*PLUS, N-acylmannosamine kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M Tascimate 5.0, 20% v/v isopropanol, 20% w/v PEG 4000, 100% v/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→45.69 Å / Num. obs: 51733 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.025 / Rrim(I) all: 0.078 / Net I/σ(I): 15 / Num. measured all: 514396 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.059.71.15737390.8720.3921.22398.5
8.95-45.698.70.0326480.9990.0110.03499.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
Aimless0.7.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JDA

6jda


Resolution: 2.002→38.77 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.76
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2294 2624 5.09 %
Rwork0.1918 --
obs0.1938 51579 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.23 Å2 / Biso mean: 43.643 Å2 / Biso min: 23.48 Å2
Refinement stepCycle: final / Resolution: 2.002→38.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4319 0 77 341 4737
Biso mean--54.56 47.72 -
Num. residues----584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0015-2.03790.34111150.31422542265798
2.0379-2.07710.35081230.27925512674100
2.0771-2.11950.26981210.258425352656100
2.1195-2.16560.27261330.240525822715100
2.1656-2.2160.26361500.232825542704100
2.216-2.27140.25361500.229725212671100
2.2714-2.33280.26651460.220625642710100
2.3328-2.40140.25141030.216925922695100
2.4014-2.47890.2481270.21325932720100
2.4789-2.56750.28151500.223925312681100
2.5675-2.67030.29021470.234825642711100
2.6703-2.79180.26311290.222725762705100
2.7918-2.93890.24991650.233125462711100
2.9389-3.12290.26661280.226125892717100
3.1229-3.36390.26321690.21125732742100
3.3639-3.70220.24141410.181225852726100
3.7022-4.23740.19021350.15226162751100
4.2374-5.33650.1691510.145526272778100
5.3365-38.77750.18381410.15462714285599

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