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- PDB-5u4h: 1.05 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosa... -

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Entry
Database: PDB / ID: 5u4h
Title1.05 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Acinetobacter baumannii in Covalently Bound Complex with (2R)-2-(phosphonooxy)propanoic Acid.
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase
KeywordsLIPID BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Lipid-Binding Protein
Function / homology
Function and homology information


UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / 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 / Ankyrin repeat profile. / Ankyrin repeat / Alpha Beta
Similarity search - Domain/homology
(2R)-2-(phosphonooxy)propanoic acid / FORMIC ACID / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.05 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Acinetobacter baumannii in Covalently Bound Complex with (2R)-2-(phosphonooxy)propanoic Acid.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_keywords
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_keywords.pdbx_keywords

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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)90,64617
Polymers89,9152
Non-polymers73115
Water21,5641197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-72 kcal/mol
Surface area29590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.289, 70.085, 78.109
Angle α, β, γ (deg.)90.00, 110.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 44957.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: murA, A7934_11825, AA954_10900, AB895_2172, AB988_1977, ABUW_3250, ACX60_14965, APD06_13410, APD31_13720, AQ480_13100, AQ482_08180, AZE33_03430, IOMTU433_3164, IX87_17660, LV38_01284
Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic
References: UniProt: A0A0R0VXX6, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-0V5 / (2R)-2-(phosphonooxy)propanoic acid


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1197 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 17.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3); Screen: JCSG+ (F8), 2.1M DL-Malic acid (pH 7.0); Cryo: 4M Sodium formate.

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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 300 mm CCD / Detector: CCD / Date: Jun 30, 2016 / 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: 1.05→20 Å / Num. obs: 357259 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 7.6 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 16.9
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.919 / % possible all: 99.4

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Processing

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

5bq2


Resolution: 1.05→19.96 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.963 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17561 17929 5 %RANDOM
Rwork0.16156 ---
obs0.16226 338746 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.965 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.13 Å2
2---0.09 Å20 Å2
3---0.29 Å2
Refinement stepCycle: 1 / Resolution: 1.05→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6286 0 41 1197 7524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197751
X-RAY DIFFRACTIONr_bond_other_d0.0020.027431
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.97810625
X-RAY DIFFRACTIONr_angle_other_deg0.84317269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4751081
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89524.419310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.025151370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.161551
X-RAY DIFFRACTIONr_chiral_restr0.0880.21236
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.029114
X-RAY DIFFRACTIONr_gen_planes_other0.0180.021513
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_it0.3980.4784064
X-RAY DIFFRACTIONr_mcbond_other0.3980.5094065
X-RAY DIFFRACTIONr_mcangle_it0.5680.7225227
X-RAY DIFFRACTIONr_mcangle_other0.5682.5895228
X-RAY DIFFRACTIONr_scbond_it0.6490.6333687
X-RAY DIFFRACTIONr_scbond_other0.6493686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8350.8975396
X-RAY DIFFRACTIONr_long_range_B_refined1.8628867
X-RAY DIFFRACTIONr_long_range_B_other1.8628868
X-RAY DIFFRACTIONr_rigid_bond_restr1.15937751
X-RAY DIFFRACTIONr_sphericity_free17.235671
X-RAY DIFFRACTIONr_sphericity_bonded4.94358021
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 1240 -
Rwork0.299 25062 -
obs--99.45 %
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)
14.7052-2.282-1.75742.48621.04423.8991-0.00430.1126-0.0039-0.0022-0.0226-0.00830.2818-0.16460.02690.0899-0.05060.0150.0362-0.01220.0181-7.583218.332424.9332
20.8939-0.3540.33250.264-0.02620.75640.0092-0.038-0.08870.061-0.00920.03790.18760.006200.0943-0.00030.01350.02490.0070.011712.268619.73145.1273
30.3918-0.0652-0.12570.40590.08661.0187-0.0082-0.01230.0150.00970.0222-0.06660.02790.1706-0.0140.0620.00820.00550.07420.0010.012226.857728.754637.4834
40.55010.122-0.02570.8686-0.03141.3151-0.0265-0.06090.04170.05090.0088-0.0243-0.0690.07560.01770.0571-0.00360.00340.038-0.00460.006318.0337.374549.2347
50.8064-0.03760.09140.2852-0.1771.41010.0119-0.02760.00210.048-0.00760.039-0.0985-0.18-0.00430.065-0.00050.02160.0613-0.00770.0105-7.538433.386339.3441
60.2331-0.066-0.10120.21170.12521.469-0.00480.0550.007-0.005-0.01170.0268-0.1424-0.16280.01650.06530.00840.00960.04790.00040.007-3.915637.302226.6369
70.3693-0.0071-0.08520.8696-0.35471.49030.01280.0802-0.0172-0.0382-0.02410.05140.0579-0.16140.01130.0544-0.00830.01210.0667-0.01250.0084-3.626928.251920.2757
81.26150.00030.06930.395-0.05691.52570.0278-0.0118-0.14740.0454-0.02120.05470.1761-0.1171-0.00660.1058-0.0380.02070.0408-0.00860.0285-3.952117.761330.8493
94.93092.2073-1.6592.7088-1.09014.1883-0.0018-0.1311-0.02650.0119-0.01930.00930.27770.15920.02110.09510.05390.01340.03770.00850.011232.459418.571111.8323
100.82540.37840.30290.2890.0420.6750.00370.033-0.0943-0.0583-0.0102-0.0410.1682-0.00130.00650.0954-0.00350.01610.0264-0.00930.016212.292519.6314-8.4688
110.50130.1079-0.03490.4112-0.05770.8937-0.0211-0.00240.0094-0.00830.01910.06620.0329-0.13540.0020.0633-0.01110.00650.0686-0.00440.0123-2.051628.7454-0.6056
120.5579-0.1391-0.05480.85420.0691.1621-0.02910.06250.0391-0.05140.00470.0228-0.0514-0.06040.02440.0561-0.00280.00340.03640.00310.00636.706937.2448-12.5519
130.76040.02980.08250.27130.1981.44170.00740.017-0.0018-0.0462-0.0039-0.0366-0.09880.1803-0.00350.0646-0.00280.02150.05820.00640.010432.307133.5426-2.6515
140.27020.0712-0.110.175-0.10891.4767-0.0039-0.05730.00760.0036-0.0074-0.0281-0.14830.15510.01130.0697-0.00930.01080.0466-0.00170.008628.651737.472810.0348
150.3262-0.0415-0.08550.83820.28811.40920.0136-0.0764-0.01130.0428-0.0253-0.05080.07120.16350.01160.05760.00680.01280.06970.01180.008728.432328.449616.4339
161.4253-0.11580.05760.440.09021.4150.03030.0072-0.1347-0.053-0.0223-0.05540.1950.1181-0.00790.11260.03820.02420.04330.01110.027528.837217.92365.8895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 13
2X-RAY DIFFRACTION2A14 - 77
3X-RAY DIFFRACTION3A78 - 152
4X-RAY DIFFRACTION4A153 - 227
5X-RAY DIFFRACTION5A228 - 279
6X-RAY DIFFRACTION6A280 - 346
7X-RAY DIFFRACTION7A347 - 394
8X-RAY DIFFRACTION8A395 - 418
9X-RAY DIFFRACTION9B-1 - 13
10X-RAY DIFFRACTION10B14 - 78
11X-RAY DIFFRACTION11B79 - 152
12X-RAY DIFFRACTION12B153 - 227
13X-RAY DIFFRACTION13B228 - 279
14X-RAY DIFFRACTION14B280 - 346
15X-RAY DIFFRACTION15B347 - 394
16X-RAY DIFFRACTION16B395 - 418

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