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- PDB-5n9m: Crystal structure of GatD - a glutamine amidotransferase from Sta... -

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Basic information

Entry
Database: PDB / ID: 5n9m
TitleCrystal structure of GatD - a glutamine amidotransferase from Staphylococcus aureus involved in peptidoglycan amidation
ComponentsCobyric acid synthase
KeywordsTRANSFERASE / Glutamine amidotransferase Peptidoglycan amidation Multidrug resistance Staphyloccocus aureus
Function / homology
Function and homology information


lipid II isoglutaminyl synthase (glutamine-hydrolysing) / carbon-nitrogen ligase activity on lipid II / glutaminase / cobalamin biosynthetic process / glutaminase activity / glutamine metabolic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape
Similarity search - Function
CobB/CobQ-like glutamine amidotransferase / Cobyric acid synthase, glutamine amidotransferase type 1 / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / CobB/CobQ-like glutamine amidotransferase domain / CobBQ-type GATase domain profile. / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
GLUTAMINE / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsLeisico, F. / Vieira, D. / Romao, M.R. / Trincao, J. / Santos-Silva, T.
Funding support Portugal, 3items
OrganizationGrant numberCountry
Fundacao para a Ciencia e TecnologiaPD/BD/105737/2014 Portugal
Fundacao para a Ciencia e TecnologiaUID/Multi/04378/2013 Portugal
Fundacao para a Ciencia e TecnologiaPTDC/QEQ-MED/1902/2014 Portugal
CitationJournal: Sci Rep / Year: 2018
Title: First insights of peptidoglycan amidation in Gram-positive bacteria - the high-resolution crystal structure of Staphylococcus aureus glutamine amidotransferase GatD.
Authors: Leisico, F. / Vieira, D.V. / Figueiredo, T.A. / Silva, M. / Cabrita, E.J. / Sobral, R.G. / Ludovice, A.M. / Trincao, J. / Romao, M.J. / de Lencastre, H. / Santos-Silva, T.
History
DepositionFeb 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cobyric acid synthase
B: Cobyric acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2764
Polymers54,9362
Non-polymers3402
Water11,259625
1
A: Cobyric acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8083
Polymers27,4681
Non-polymers3402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cobyric acid synthase


Theoretical massNumber of molelcules
Total (without water)27,4681
Polymers27,4681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.610, 93.920, 110.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cobyric acid synthase


Mass: 27468.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Gene: SACOL1950 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2WZ38
#2: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10N2O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 30%(w/v) PEG 400, 100 mM sodium acetate/ acetic acid pH 4.5, 200 mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→36.44 Å / Num. obs: 42987 / % possible obs: 97.9 % / Redundancy: 21.7 % / Rpim(I) all: 0.022 / Net I/σ(I): 2.2
Reflection shellResolution: 1.85→1.893 Å / Redundancy: 20.1 % / Mean I/σ(I) obs: 5.2 / Rpim(I) all: 0.149 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→36.435 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.59
RfactorNum. reflection% reflection
Rfree0.1863 2169 5.05 %
Rwork0.1486 --
obs0.1505 42922 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→36.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3830 0 23 625 4478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063991
X-RAY DIFFRACTIONf_angle_d0.9945378
X-RAY DIFFRACTIONf_dihedral_angle_d12.8621521
X-RAY DIFFRACTIONf_chiral_restr0.038579
X-RAY DIFFRACTIONf_plane_restr0.005710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89310.33321330.2592318X-RAY DIFFRACTION85
1.8931-1.94040.27861470.22152466X-RAY DIFFRACTION90
1.9404-1.99290.2281390.19032558X-RAY DIFFRACTION95
1.9929-2.05150.20361300.17422712X-RAY DIFFRACTION98
2.0515-2.11770.2151580.16252742X-RAY DIFFRACTION100
2.1177-2.19340.18871200.15162752X-RAY DIFFRACTION100
2.1934-2.28120.20951440.14872742X-RAY DIFFRACTION100
2.2812-2.3850.1881360.1452755X-RAY DIFFRACTION100
2.385-2.51070.19561580.14622756X-RAY DIFFRACTION100
2.5107-2.6680.18861570.15512767X-RAY DIFFRACTION100
2.668-2.87390.20041490.15732759X-RAY DIFFRACTION100
2.8739-3.16290.18161390.15292798X-RAY DIFFRACTION100
3.1629-3.62030.17271390.13522824X-RAY DIFFRACTION100
3.6203-4.55980.15191560.11642828X-RAY DIFFRACTION100
4.5598-36.44180.15711640.13792976X-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)
10.94580.88121.01826.27964.21935.45030.0486-0.1976-0.18370.32420.122-0.28440.35310.3189-0.17690.18820.0584-0.02460.31140.01720.168721.669579.392286.5353
20.77791.2385-0.76162.7836-0.75830.99310.0757-0.2514-0.08130.03510.0325-0.26890.17630.3239-0.07030.18870.0388-0.06780.296-0.02580.136130.023284.564487.4109
31.749-0.2875-0.67912.70421.80112.63860.0034-0.1775-0.09490.214-0.04960.10860.1928-0.1280.04660.1508-0-0.01140.19140.01110.129712.572180.506582.1255
43.02381.0180.50265.99033.29336.4306-0.0413-0.0027-0.5090.0618-0.27530.40570.5946-0.61140.21960.1898-0.04550.04370.1707-0.00340.25045.584869.451770.0624
51.5984-0.1586-0.14561.40110.16480.6763-0.00530.0002-0.10880.0105-0.0144-0.02130.0440.03980.01050.15790.0154-0.00770.16540.00290.145321.011877.582665.8998
63.9239-1.25330.96273.17520.82321.39360.026-0.10710.44020.05820.0666-0.2036-0.23770.2756-0.07170.1857-0.04140.00590.2176-0.05230.207230.690493.113679.4904
73.42341.148-1.33037.52032.02042.7651-0.31730.1543-0.3593-0.1780.3052-0.1390.038-0.0792-0.03580.16250.02180.0090.3251-0.0510.28538.37475.102263.2884
80.78140.3555-0.67013.7793-0.96880.7040.0004-0.0237-0.3149-0.14290.031-0.11230.94640.2838-0.50950.34430.09470.07550.2355-0.00940.251818.25477.7238109.4336
90.93611.54150.77884.96680.74182.3112-0.0973-0.1831-0.2770.18440.0542-0.41590.32510.52670.03280.27430.1330.03430.29490.0210.313927.924280.773112.2489
101.37390.2277-0.01282.538-1.93332.731-0.0125-0.1235-0.55330.15090.0904-0.02190.7212-0.0666-0.10020.41150.04790.03680.18850.03480.293413.6575.8347115.55
113.7311.84481.64662.9943-0.53033.1379-0.0624-0.0278-0.25420.1039-0.06630.04750.5949-0.42630.03060.2255-0.0250.08980.1464-0.00070.22635.418978.3476114.101
123.12060.1440.71052.19280.41112.0092-0.22360.152-0.1482-0.16660.07420.19850.5703-0.3657-0.11830.2539-0.09070.02730.2252-0.01290.17333.165386.4939107.9662
131.75840.164-0.56481.05390.05212.015-0.04530.0816-0.0164-0.04450.02390.02180.0374-0.04840.02630.15770.00950.00620.1403-0.00190.147110.359896.4765106.9561
141.7995-0.5430.53132.08320.60670.4695-0.0843-0.32070.05460.227-0.03-0.37950.19510.78950.11720.20.0626-0.0270.40110.03610.249928.051590.1195119.4162
155.4518-3.75763.71396.48-5.08917.7838-0.10690.2607-0.1173-0.5152-0.1974-0.31810.58450.42870.34240.2596-0.03570.06790.2168-0.01650.242826.8945102.354998.9712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 100 )
4X-RAY DIFFRACTION4chain 'A' and (resid 101 through 113 )
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 196 )
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 222 )
7X-RAY DIFFRACTION7chain 'A' and (resid 223 through 243 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 19 )
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 42 )
10X-RAY DIFFRACTION10chain 'B' and (resid 43 through 62 )
11X-RAY DIFFRACTION11chain 'B' and (resid 63 through 86 )
12X-RAY DIFFRACTION12chain 'B' and (resid 87 through 113 )
13X-RAY DIFFRACTION13chain 'B' and (resid 114 through 196 )
14X-RAY DIFFRACTION14chain 'B' and (resid 197 through 222 )
15X-RAY DIFFRACTION15chain 'B' and (resid 223 through 239 )

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