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- PDB-5vat: Haemophilus influenzae LpoA: Monoclinic form (Mon2) with 2 molecu... -

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Basic information

Entry
Database: PDB / ID: 5vat
TitleHaemophilus influenzae LpoA: Monoclinic form (Mon2) with 2 molecules per a.u.
ComponentsPenicillin-binding protein activator LpoA
KeywordsBIOSYNTHETIC PROTEIN / lipoprotein / conformational flexibility / PBP1A / binding protein
Function / homologyPenicillin-binding protein activator LpoA / LppC putative lipoprotein / periplasmic side of cell outer membrane / enzyme regulator activity / peptidoglycan biosynthetic process / Periplasmic binding protein-like I / Tetratricopeptide-like helical domain superfamily / regulation of cell shape / Penicillin-binding protein activator LpoA
Function and homology information
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSaper, M.A. / Sathiyamoorthy, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI099984 United States
Citation
Journal: J. Biol. Chem. / Year: 2017
Title: Structural analyses of the Haemophilus influenzae peptidoglycan synthase activator LpoA suggest multiple conformations in solution.
Authors: Sathiyamoorthy, K. / Vijayalakshmi, J. / Tirupati, B. / Fan, L. / Saper, M.A.
#1: Journal: Proteins / Year: 2008
Title: Structure of YraM, a protein essential for growth of Haemophilus influenzae.
Authors: Vijayalakshmi, J. / Akerley, B.J. / Saper, M.A.
History
DepositionMar 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein activator LpoA
B: Penicillin-binding protein activator LpoA


Theoretical massNumber of molelcules
Total (without water)121,0522
Polymers121,0522
Non-polymers00
Water2,468137
1
A: Penicillin-binding protein activator LpoA


Theoretical massNumber of molelcules
Total (without water)60,5261
Polymers60,5261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein activator LpoA


Theoretical massNumber of molelcules
Total (without water)60,5261
Polymers60,5261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.935, 72.695, 120.572
Angle α, β, γ (deg.)90.000, 94.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 34 through 103 or resid 105...
21(chain B and (resid 34 through 103 or resid 105...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEILEILE(chain A and (resid 34 through 103 or resid 105...AA34 - 1032 - 71
12ALAALAVALVAL(chain A and (resid 34 through 103 or resid 105...AA105 - 15573 - 123
13ALAALAASPASP(chain A and (resid 34 through 103 or resid 105...AA157 - 176125 - 144
14THRTHRGLYGLY(chain A and (resid 34 through 103 or resid 105...AA178 - 285146 - 253
15SERSERLEULEU(chain A and (resid 34 through 103 or resid 105...AA287 - 355255 - 323
16TYRTYRASNASN(chain A and (resid 34 through 103 or resid 105...AA357 - 575325 - 543
21PHEPHEILEILE(chain B and (resid 34 through 103 or resid 105...BB34 - 1032 - 71
22ALAALAVALVAL(chain B and (resid 34 through 103 or resid 105...BB105 - 15573 - 123
23ALAALAASPASP(chain B and (resid 34 through 103 or resid 105...BB157 - 176125 - 144
24THRTHRGLYGLY(chain B and (resid 34 through 103 or resid 105...BB178 - 285146 - 253
25SERSERLEULEU(chain B and (resid 34 through 103 or resid 105...BB287 - 355255 - 323
26TYRTYRASNASN(chain B and (resid 34 through 103 or resid 105...BB357 - 429325 - 397
27THRTHRASNASN(chain B and (resid 34 through 103 or resid 105...BB433 - 575401 - 543

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Components

#1: Protein Penicillin-binding protein activator LpoA / PBP activator LpoA


Mass: 60525.926 Da / Num. of mol.: 2 / Fragment: UNP residues 33-575
Source method: isolated from a genetically manipulated source
Details: Expressed without His6 tag Four MET modeled as MSE due to difference electron density
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: lpoA, HI_1655 / Plasmid: pETBlue-2 / Details (production host): His6 tag removed / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3)/pLacI / References: UniProt: P45299
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: One microliter of concentrated protein (33 mg/ml in 150 mm NaCl, 50 mm Tris-HCl, ph 8.0) and one microliter precipitant (8% polyethylene glycol 4000, 0.1 m sodium acetate trihydrate, ph 4.6) ...Details: One microliter of concentrated protein (33 mg/ml in 150 mm NaCl, 50 mm Tris-HCl, ph 8.0) and one microliter precipitant (8% polyethylene glycol 4000, 0.1 m sodium acetate trihydrate, ph 4.6) and 0.2 microliter 30% xylitol. Cryoprotectant: precipitant solution containing 15% glycerol.
PH range: 5.5-7.4

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07806 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 8, 2009 / Details: MONOCHROMATOR
RadiationMonochromator: Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07806 Å / Relative weight: 1
ReflectionResolution: 2.49→100 Å / Num. obs: 45736 / % possible obs: 87.09 % / Redundancy: 2.66 % / Biso Wilson estimate: 39.5642078485 Å2 / CC1/2: 0.9 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.061 / Rrim(I) all: 0.107 / Χ2: 1.08 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible allMean I/σ(I) obs
2.49-2.532.20.51318870.6350.3890.6470.95365.1
2.53-2.592.40.48625300.6640.3610.6091.01686.1
2.59-2.642.50.425380.7450.2970.5011.01788.52.31
2.64-2.72.50.37826150.750.2790.4721.03290.2
2.7-2.772.50.3426450.790.2490.4241.06291.1
2.77-2.852.60.28126100.8640.2030.3481.06790.8
2.85-2.932.60.23526660.930.1690.2911.09591
2.93-3.022.60.20426150.9160.1460.2521.190.6
3.02-3.132.60.17326200.9330.1250.2141.16589.8
3.13-3.262.70.13925950.9540.0990.1721.18589.6
3.26-3.412.70.11225900.970.080.1381.24188.9
3.41-3.592.70.09125480.9780.0650.1131.26288.2
3.59-3.812.70.08125540.9820.0570.0991.2287.6
3.81-4.12.70.07525300.9840.0520.0911.26186.3
4.1-4.522.80.06825250.9870.0470.0831.21785.9
4.52-5.172.90.05925090.990.040.0710.9786
5.17-6.512.90.05225790.9920.0350.0630.82987
6.51-46.42.80.05925800.9880.040.0710.90485.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å46.41 Å
Translation2.5 Å46.41 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-20000.98data reduction
HKL-20000.98data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CKM, 4P29

3ckm

4p29


Resolution: 2.6→42.341 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2568 3153 4.36 %
Rwork0.2233 69156 -
obs0.2247 72309 81.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 245.79 Å2 / Biso mean: 73.3186 Å2 / Biso min: 11.9 Å2
Refinement stepCycle: final / Resolution: 2.6→42.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8410 0 0 137 8547
Biso mean---42.56 -
Num. residues----1082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028598
X-RAY DIFFRACTIONf_angle_d0.54211697
X-RAY DIFFRACTIONf_chiral_restr0.0391329
X-RAY DIFFRACTIONf_plane_restr0.0031556
X-RAY DIFFRACTIONf_dihedral_angle_d9.1325253
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5948X-RAY DIFFRACTION8.578TORSIONAL
12B5948X-RAY DIFFRACTION8.578TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.63880.35061210.33282933305480
2.6388-2.680.38571390.33453036317582
2.68-2.7240.42311320.33463038317083
2.724-2.77090.34211400.32033047318783
2.7709-2.82130.36081530.30953075322883
2.8213-2.87560.33991220.30173047316983
2.8756-2.93420.35311440.29483067321183
2.9342-2.9980.32321410.30193065320683
2.998-3.06770.30321470.28473013316083
3.0677-3.14440.2731380.26493024316282
3.1444-3.22940.24641330.26632999313282
3.2294-3.32440.28251260.24563047317382
3.3244-3.43170.29731580.23062959311781
3.4317-3.55430.25041400.23722985312581
3.5543-3.69650.24381400.2222987312781
3.6965-3.86460.22921420.20232922306480
3.8646-4.06820.22651300.20072950308080
4.0682-4.32290.19861390.18492966310580
4.3229-4.65630.21311260.18362952307880
4.6563-5.12410.20991410.18922947308881
5.1241-5.86390.31781290.1953000312982
5.8639-7.38160.2381400.19273077321783
7.3816-42.3470.18741320.16613020315282
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)
15.2374-4.0451-0.62265.08160.2790.4276-0.0119-0.12770.23170.03320.10510.1937-0.2563-0.0889-0.06490.4242-0.005-0.01930.3749-0.02860.384413.4751-15.31542.6725
20.51090.3355-0.17641.2644-0.44473.714-0.0201-0.1479-0.08660.2365-0.0918-0.3221-0.00020.07270.10580.4362-0.0383-0.07280.41850.06490.625854.1418-17.906421.012
33.4139-1.86310.27822.6721-0.24790.3463-0.0918-0.1285-0.22590.24110.10750.02670.16060.0267-0.020.38580.0023-0.01330.26190.00130.307732.3413-15.6471-57.8367
44.1102-2.26410.66484.59751.74963.7447-0.1321-0.30410.05390.1062-0.02250.3316-0.1636-0.3220.21670.3478-0.03640.00260.31740.02740.4316-14.2758-17.6882-53.6671
50.9809-1.09811.35221.28-0.92758.4499-0.046-0.2877-0.08440.38740.078-0.20720.1170.0915-0.03010.5277-0.1301-0.10920.4725-0.02630.6012-0.6926-16.0159-31.2058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 33 through 246 )B33 - 246
2X-RAY DIFFRACTION2chain 'B' and (resid 247 through 575 )B247 - 575
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 257 )A33 - 257
4X-RAY DIFFRACTION4chain 'A' and (resid 258 through 354 )A258 - 354
5X-RAY DIFFRACTION5chain 'A' and (resid 355 through 575 )A355 - 575

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