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- PDB-4fo1: Crystal structure of lincosamide antibiotic adenylyltransferase L... -

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Basic information

Entry
Database: PDB / ID: 4fo1
TitleCrystal structure of lincosamide antibiotic adenylyltransferase LnuA, apo
ComponentsLincosamide resistance protein
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / ANTIBIOTIC RESISTANCE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID) / NIAID / National Institute of Allergy and Infectious Diseases / ALPHA+BETA STRUCTURE / AMINOGLYCOSIDE-2''-ADENYLYLTRANSFERASE SUPERFAMILY / NUCLEOTIDYLTRANSFERASE SUPERFAMILY / LINCOSAMIDE ADENYLYLTRANSFERASE / LINCOSAMIDE ANTIBIOTICS / LINCOMYCIN / CLINDAMYCIN / ADENOSINE TRIPHOSPHATE / INTRACELLULAR
Function / homologyAminoglycoside-2''-adenylyltransferase / Aminoglycoside-2''-adenylyltransferase / Beta Polymerase; domain 2 - #40 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / response to antibiotic / 2-Layer Sandwich / Alpha Beta / Lincosamide resistance protein
Function and homology information
Biological speciesStaphylococcus haemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsStogios, P.J. / Wawrzak, Z. / Minasov, G. / Evdokimova, E. / Egorova, O. / Kudritska, M. / Yim, V. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of lincosamide antibiotic adenylyltransferase LnuA, apo
Authors: Stogios, P.J. / Wawrzak, Z. / Minasov, G. / Evdokimova, E. / Egorova, O. / Kudritska, M. / Yim, V. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJun 20, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionJul 4, 2012ID: 4E8I
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Structure summary
Revision 1.2May 7, 2014Group: Other
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Nov 6, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Lincosamide resistance protein
B: Lincosamide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4616
Polymers38,5082
Non-polymers9534
Water4,017223
1
A: Lincosamide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7303
Polymers19,2541
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lincosamide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7303
Polymers19,2541
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.389, 61.910, 61.341
Angle α, β, γ (deg.)90.00, 103.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lincosamide resistance protein


Mass: 19253.844 Da / Num. of mol.: 2 / Fragment: LnuA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus haemolyticus (bacteria) / Gene: linA / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06107
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 1.4 M SODIUM CITRATE, 0.1 M HEPES PH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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 16, 2011 / Details: MIRRORS
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→29.855 Å / Num. obs: 28239 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 7.7 % / Rsym value: 0.129 / Net I/σ(I): 15.76
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 3.75 / Rsym value: 0.569 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.solve)model building
PHENIX(phenix.refine: 1.8_1066)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→29.855 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2622 1109 4.97 %random
Rwork0.2153 ---
obs0.2178 22329 97.35 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→29.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2639 0 60 223 2922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032822
X-RAY DIFFRACTIONf_angle_d0.7633828
X-RAY DIFFRACTIONf_dihedral_angle_d17.3431075
X-RAY DIFFRACTIONf_chiral_restr0.051389
X-RAY DIFFRACTIONf_plane_restr0.002489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.24790.35471300.24992505X-RAY DIFFRACTION92
2.2479-2.36630.30241310.24292570X-RAY DIFFRACTION95
2.3663-2.51450.26351410.23552588X-RAY DIFFRACTION97
2.5145-2.70850.25481330.23692659X-RAY DIFFRACTION98
2.7085-2.98090.30261420.23442677X-RAY DIFFRACTION99
2.9809-3.41170.25291460.20832710X-RAY DIFFRACTION99
3.4117-4.29630.22531410.17822723X-RAY DIFFRACTION100
4.2963-29.85810.2471450.21332788X-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)
13.29371.195-0.312.4757-0.61612.3744-0.0366-0.2554-0.05140.1935-0.0146-0.09690.09020.27970.04810.28320.0732-0.01240.30710.00040.218142.534534.013931.353
22.30340.52720.51475.36721.03762.1236-0.21610.18540.132-0.08260.06380.0055-0.06540.16890.17810.289-0.0214-0.0030.26490.05130.147139.341343.258819.8864
32.1792-0.8793-0.35462.92591.15892.85170.03610.23170.0348-0.122-0.00680.20660.0451-0.2025-0.01760.2598-0.0022-0.0230.32460.05170.271724.83725.33127.0899
41.48040.79530.43095.66140.442.35610.1340.00620.04870.0506-0.02460.0150.30090.1446-0.09170.26820.0543-0.05690.3520.00320.30634.7873-3.977813.5185
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 4:94
2X-RAY DIFFRACTION2chain A and resi 95:161
3X-RAY DIFFRACTION3chain B and resi 4:94
4X-RAY DIFFRACTION4chain B and resi 95:161

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