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- PDB-4n3o: 2.4 Angstrom Resolution Crystal Structure of Putative Sugar Kinas... -

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Basic information

Entry
Database: PDB / ID: 4n3o
Title2.4 Angstrom Resolution Crystal Structure of Putative Sugar Kinase from Campylobacter jejuni.
ComponentsPutative D-glycero-D-manno-heptose 7-phosphate kinase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


D-glycero-alpha-D-manno-heptose-7-phosphate kinase / D-glycero-D-manno-heptose 7-phosphate metabolic process / nucleotide-sugar biosynthetic process / galactokinase activity / capsule polysaccharide biosynthetic process / galactose metabolic process / kinase activity / magnesium ion binding / ATP binding / cytosol
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-alpha-D-manno-heptose 7-phosphate kinase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsMinasov, G. / Wawrzak, Z. / Gordon, E. / Onopriyenko, O. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.4 Angstrom Resolution Crystal Structure of Putative Sugar Kinase from Campylobacter jejuni.
Authors: Minasov, G. / Wawrzak, Z. / Gordon, E. / Onopriyenko, O. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative D-glycero-D-manno-heptose 7-phosphate kinase
B: Putative D-glycero-D-manno-heptose 7-phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4393
Polymers77,3992
Non-polymers401
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-16 kcal/mol
Surface area28960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.609, 85.796, 77.947
Angle α, β, γ (deg.)90.00, 122.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative D-glycero-D-manno-heptose 7-phosphate kinase


Mass: 38699.352 Da / Num. of mol.: 2 / Fragment: Putative Sugar Kinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: hddA, Cj1425c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q0P8I9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein: 1.5mg/mL, 0.3M Sodium cloride, 0.1M HEPES pH 7.5; Screen: 0.2M Calcium acetate, 0.1M Na Cacodylate pH 6.0, 18% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2009 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 26058 / Num. obs: 26058 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 40.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1337 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.8.0046refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→29.16 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 16.126 / SU ML: 0.187
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.54 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23229 1317 5.1 %RANDOM
Rwork0.17693 ---
all0.17973 24593 --
obs0.17973 24593 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.502 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å2-0 Å20.67 Å2
2---1.16 Å2-0 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 1 138 5227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195272
X-RAY DIFFRACTIONr_bond_other_d0.0010.025045
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9667105
X-RAY DIFFRACTIONr_angle_other_deg0.7311616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.6755653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.56123.95238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.78715915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2281529
X-RAY DIFFRACTIONr_chiral_restr0.0820.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.025978
X-RAY DIFFRACTIONr_gen_planes_other0.0160.021247
X-RAY DIFFRACTIONr_mcbond_it3.1644.22603
X-RAY DIFFRACTIONr_mcbond_other3.1644.1992602
X-RAY DIFFRACTIONr_mcangle_it5.0196.2733259
X-RAY DIFFRACTIONr_mcangle_other5.0186.2733260
X-RAY DIFFRACTIONr_scbond_it3.514.4432668
X-RAY DIFFRACTIONr_scbond_other3.514.4442668
X-RAY DIFFRACTIONr_scangle_other5.5616.513846
X-RAY DIFFRACTIONr_long_range_B_refined8.45333.9276224
X-RAY DIFFRACTIONr_long_range_B_other8.42733.8326178
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 92 -
Rwork0.229 1822 -
obs-1822 100 %
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)
13.2428-0.24410.2351.87181.0761.71060.1272-0.3391-0.2710.20650.0761-0.33920.27190.3869-0.20330.06740.0599-0.0680.1930.0150.136318.860520.728117.1968
25.75182.4963-0.32199.57311.3510.68280.23260.2115-0.4335-0.3859-0.1299-0.22660.03490.315-0.10270.18340.1506-0.07390.3593-0.0740.268121.044616.2989.6048
33.609-0.91221.5831.6733-0.81741.45390.33330.3756-1.03350.0593-0.147-0.11080.38060.4226-0.18620.29880.1175-0.05780.2101-0.06160.48238.16667.81599.5929
41.611-1.3134-0.0462.1647-0.47234.581-0.0918-0.1156-0.6312-0.03090.20550.28470.4965-0.1747-0.11370.0686-0.0090.02850.03580.02470.3125-6.86529.325817.6952
53.88060.3018-0.79761.03430.38221.2784-0.1208-0.1524-0.16540.05090.12780.15870.1548-0.0459-0.0070.11930.07680.00120.10960.05230.0841-5.882421.483423.8229
62.2491-0.1287-0.53661.3138-0.62211.16620.0838-0.22960.1037-0.03850.0850.178-0.1831-0.2174-0.16880.05730.05340.01850.10990.01460.0545-21.314539.144914.7357
75.86930.19591.13262.98340.11082.49030.09450.24470.5064-0.30170.02060.0634-0.2702-0.2491-0.11510.11830.08330.07220.09620.07260.1193-20.236742.393510.2589
82.30710.00920.46161.4221-0.6651.85280.0199-0.21840.7857-0.08780.0627-0.0353-0.30410.0254-0.08260.1179-0.0040.09050.0562-0.07590.32750.641350.116710.4249
93.3976-0.1131.28966.9067-3.33454.88980.1539-0.7560.39660.5006-0.0321-0.1014-0.61990.0752-0.12170.1257-0.06430.03890.3356-0.23830.18427.662445.629327.3864
105.49711.01282.43091.40240.88723.44590.3853-0.5074-0.07710.0719-0.1449-0.08570.1597-0.1762-0.24040.06960.00170.01650.09040.0160.0394-4.462833.284518.8245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 127
2X-RAY DIFFRACTION2A128 - 153
3X-RAY DIFFRACTION3A154 - 179
4X-RAY DIFFRACTION4A180 - 279
5X-RAY DIFFRACTION5A280 - 339
6X-RAY DIFFRACTION6B-2 - 108
7X-RAY DIFFRACTION7B109 - 153
8X-RAY DIFFRACTION8B154 - 252
9X-RAY DIFFRACTION9B253 - 317
10X-RAY DIFFRACTION10B318 - 339

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