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- PDB-5ujs: 2.45 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosa... -

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Basic information

Entry
Database: PDB / ID: 5ujs
Title2.45 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Campylobacter jejuni.
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase
KeywordsHYDROLASE / OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / UDP-N-acetylglucosamine 1-carboxyvinyltransferase.
Function / homology
Function and homology information


UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / cytoplasm
Similarity search - Function
UDP-N-acetylglucosamine 1-carboxyvinyltransferase / : / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Alpha Beta
Similarity search - Domain/homology
UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Stam, J. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.45 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Campylobacter jejuni.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Stam, J. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0003
Polymers95,9642
Non-polymers351
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-33 kcal/mol
Surface area31600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.258, 86.024, 80.421
Angle α, β, γ (deg.)90.00, 109.28, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: -1 - 417 / Label seq-ID: 23 - 441

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Enoylpyruvate transferase / UDP-N-acetylglucosamine enolpyruvyl transferase / EPT


Mass: 47982.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: murA, Cj0858c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9PP65, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 7.7 mg/ml, 0.25M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: PEG II (D1), 0.1M Sodium acetate, 0.1 HEPES (pH 7.5), 22% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2009 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 29963 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 56.4 Å2 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.045 / Rsym value: 0.075 / Χ2: 1.011 / Net I/σ(I): 15.2
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1348 / CC1/2: 0.77 / Rrim(I) all: 0.34 / Rsym value: 0.538 / Χ2: 1 / % possible all: 87.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BQ2

5bq2


Resolution: 2.46→29.93 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 29.822 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R: 1.087 / ESU R Free: 0.335 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27456 1442 4.8 %RANDOM
Rwork0.22426 ---
obs0.22661 28521 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.486 Å2
Baniso -1Baniso -2Baniso -3
1-3.5 Å20 Å2-6.15 Å2
2---0.36 Å20 Å2
3---0.93 Å2
Refinement stepCycle: 1 / Resolution: 2.46→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6427 0 1 202 6630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196559
X-RAY DIFFRACTIONr_bond_other_d0.0010.026410
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9838869
X-RAY DIFFRACTIONr_angle_other_deg0.894314898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.1035856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.35925.923260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.238151227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.3521524
X-RAY DIFFRACTIONr_chiral_restr0.0810.21074
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.027249
X-RAY DIFFRACTIONr_gen_planes_other0.0210.021147
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5062.7473418
X-RAY DIFFRACTIONr_mcbond_other1.5062.7463417
X-RAY DIFFRACTIONr_mcangle_it2.6144.114276
X-RAY DIFFRACTIONr_mcangle_other2.6134.1124277
X-RAY DIFFRACTIONr_scbond_it1.4273.0153141
X-RAY DIFFRACTIONr_scbond_other1.4263.0123138
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4284.4214592
X-RAY DIFFRACTIONr_long_range_B_refined6.43933.197133
X-RAY DIFFRACTIONr_long_range_B_other6.42133.1127114
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23666 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.459→2.522 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 94 -
Rwork0.34 1726 -
obs--80.89 %
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)
12.91362.895-1.31434.4525-4.29086.2534-0.4786-0.17-0.2673-0.80380.6661-0.11560.8219-1.4809-0.18750.1976-0.14240.03890.47060.03890.1733-5.64692.707117.0626
24.2592-3.12681.45524.7869-0.7190.73810.4186-0.2046-0.3468-0.0953-0.3510.32520.3186-0.31-0.06760.2994-0.12090.15790.29890.04750.220913.1454-3.3839.1344
32.1922-1.14851.5742.3612-1.22432.01740.0053-0.17190.17190.2854-0.192-0.02540.0045-0.22010.18670.1356-0.05710.12310.1385-0.03650.15818.561911.621135.1925
43.5371.1810.4683.3758-0.58763.60460.10520.13120.0361-0.3381-0.0419-0.03750.33940.1802-0.06340.07640.01310.01880.0352-0.02150.03174.088412.15715.2922
51.62550.26812.16333.39240.37643.11880.05420.2427-0.3450.07670.1149-0.3410.25390.3719-0.16910.18270.19780.2060.6897-0.00390.444539.7623-7.15245.5568
62.35830.6681.94361.19220.72783.2885-0.02470.30160.1279-0.5047-0.1883-0.0630.06950.48890.2130.31950.14580.16390.38480.01960.224230.02784.05563.7415
73.8697-2.43030.94893.1268-1.55487.405-0.29840.1668-0.09220.2336-0.0546-0.1717-0.16220.11710.35290.03090.00530.0160.06280.0450.09640.609415.731126.0269
86.5279-0.18480.53274.54670.52714.52690.06340.4396-0.70960.3936-0.0068-0.26590.40450.3793-0.05670.08920.11220.00560.30530.06030.141550.80371.552721.1529
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 9
2X-RAY DIFFRACTION2A10 - 115
3X-RAY DIFFRACTION3A116 - 306
4X-RAY DIFFRACTION4A307 - 418
5X-RAY DIFFRACTION5B-12 - 79
6X-RAY DIFFRACTION6B80 - 310
7X-RAY DIFFRACTION7B311 - 358
8X-RAY DIFFRACTION8B359 - 418

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