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- PDB-3zh4: crystal structure of S. pneumoniae Hungary 19A MurA1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 3zh4
Titlecrystal structure of S. pneumoniae Hungary 19A MurA1 in complex with citrate
ComponentsUDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE
KeywordsTRANSFERASE / MURA
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 / cytosol
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
CITRATE ANION / DI(HYDROXYETHYL)ETHER / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGutierrez-Fernandez, J. / Hermoso, J.A.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: Heteroresistance to Fosfomycin is Predominant in Streptococcus Pneumoniae and Depends on Mura1 Gene.
Authors: Engel, H. / Gutierrez-Fernandez, J. / Fluckiger, C. / Martinez-Ripoll, M. / Muhlemann, K. / Hermoso, J.A. / Hilty, M. / Hathaway, L.J.
History
DepositionDec 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3983
Polymers45,1031
Non-polymers2952
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.584, 70.360, 45.241
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE / ENOYLPYRUVATE TRANSFERASE / UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE


Mass: 45102.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: HUNGARY 19A-6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: B1IBM3, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 1.86 Å3/Da / Density % sol: 33.9 % / Description: NONE
Crystal growpH: 5.6
Details: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE, PH 5.6, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→45.2 Å / Num. obs: 32208 / % possible obs: 99.7 % / Observed criterion σ(I): 2.3 / Redundancy: 12.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 13 % / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NAW

1naw


Resolution: 1.8→45.241 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 19.94 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE NOT INCLUDED IN THE MODEL
RfactorNum. reflection% reflection
Rfree0.2042 1634 5.1 %
Rwork0.1603 --
obs0.1626 32208 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 20 347 3473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073199
X-RAY DIFFRACTIONf_angle_d1.074337
X-RAY DIFFRACTIONf_dihedral_angle_d12.8491203
X-RAY DIFFRACTIONf_chiral_restr0.067518
X-RAY DIFFRACTIONf_plane_restr0.004564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8004-1.85340.30741340.23422420X-RAY DIFFRACTION97
1.8534-1.91320.26341350.20962500X-RAY DIFFRACTION100
1.9132-1.98160.26191340.19292525X-RAY DIFFRACTION100
1.9816-2.0610.21771230.17232545X-RAY DIFFRACTION100
2.061-2.15470.23081360.16782508X-RAY DIFFRACTION100
2.1547-2.26830.21381480.15662524X-RAY DIFFRACTION100
2.2683-2.41050.21851210.1552546X-RAY DIFFRACTION100
2.4105-2.59660.20231170.16372561X-RAY DIFFRACTION100
2.5966-2.85780.21521490.16532533X-RAY DIFFRACTION100
2.8578-3.27120.18331470.16232572X-RAY DIFFRACTION100
3.2712-4.1210.19211420.13572617X-RAY DIFFRACTION100
4.121-45.25530.17271480.15022724X-RAY DIFFRACTION100
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)
12.0850.30670.98180.66180.30871.31480.0945-0.3103-0.10120.1004-0.05160.06370.0947-0.1473-0.02290.1056-0.01270.02250.09940.02820.072-11.571119.4173-2.9951
24.476-0.37191.50141.1624-0.31982.73340.0963-0.2546-0.42380.2064-0.06110.01890.28020.0023-0.00240.21590.00460.00680.18060.07730.1464-1.513218.84367.3332
31.8814-0.5503-1.31272.17050.49411.81450.11150.0081-0.96280.0546-0.1667-0.07660.64940.0948-0.00770.23630.0288-0.03680.17420.03160.31947.542810.1255-2.9327
42.6784-0.5112-0.23412.12240.07011.7834-0.0848-0.0683-0.28360.02090.0585-0.0740.18410.23580.02270.0832-0.00130.01310.13890.00890.098811.810818.5774-9.7576
51.08040.13710.77010.8970.40771.0614-0.05090.04250.0503-0.12680.00320.0793-0.12960.0650.06020.0882-0.0150.01130.05780.01210.078-13.432625.7603-19.4512
61.73320.40430.38021.0827-0.07192.07330.1269-0.0589-0.20180.0214-0.03690.00220.2073-0.0042-0.02280.107-0.0045-0.00930.03920.01030.1184-20.24369.052-18.4234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 59 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 60 THROUGH 91 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 92 THROUGH 121 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 122 THROUGH 218 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 219 THROUGH 304 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 305 THROUGH 419 )

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