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- PDB-3ckm: LpoA (YraM) C-domain from Haemophilus influenzae, a regulator of PBP1A -

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Basic information

Entry
Database: PDB / ID: 3ckm
TitleLpoA (YraM) C-domain from Haemophilus influenzae, a regulator of PBP1A
ComponentsYRAM (HI1655)
KeywordsBIOSYNTHETIC PROTEIN / YraM / periplasmic-binding protein / lipoprotein / unliganded / PBP1A / TRANSPEPTIDASE / PEPTIDOGLYCAN
Function / homology
Function and homology information


periplasmic side of cell outer membrane / peptidoglycan biosynthetic process / enzyme regulator activity / regulation of cell shape
Similarity search - Function
Penicillin-binding protein activator LpoA / LppC putative lipoprotein / Response regulator / Periplasmic binding protein-like I / Tetratricopeptide-like helical domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Penicillin-binding protein activator LpoA
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsVijayalakshmi, J. / Saper, M.A.
Citation
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.
#1: 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.
History
DepositionMar 16, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionMay 13, 2008ID: 2H4A
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_database_related / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct / struct_keywords
Item: _struct.title / _struct_keywords.text
Revision 1.3Mar 26, 2025Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: YRAM (HI1655)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3993
Polymers36,2251
Non-polymers1742
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.907, 50.644, 63.676
Angle α, β, γ (deg.)90.00, 106.73, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-917-

HOH

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Components

#1: Protein YRAM (HI1655) / LpoA


Mass: 36225.055 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 256-573
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: Rd KW20 / Gene: YraM / Plasmid: pETBlue-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami (DE3) pLacI / References: UniProt: P45299
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CHEMICAL IDENTITY OF BME A 583 IS UNKNOWN BUT MODELED AS BETA-MERCAPTOETHANOL
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: 2.34 Å3/Da / Density % sol: 47.49 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.0M Li sulfate monohydrate, 2% W/V PEG 8000 and 0.05% BME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 165 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.97857,0.97843,0.96321
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 28, 2004 / Details: Si(111)Monochromator
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978571
20.978431
30.963211
ReflectionRedundancy: 5.58 % / Av σ(I) over netI: 10.8 / Number: 596801 / Rmerge(I) obs: 0.095 / Χ2: 1.51 / D res high: 1.09 Å / D res low: 47.1 Å / Num. obs: 106384 / % possible obs: 76.7
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
2.3547.198.70.0713.666.121377
1.872.351000.0991.86.22929
1.631.8799.90.1721.156.16667
1.481.6399.70.2910.986.13284
1.381.4899.30.4590.946.15107
1.291.3897.70.5840.955.7252
1.231.2977.90.6320.934.2117
1.181.23530.6740.963.6410
1.131.1829.90.7050.983.347
1.091.1310.10.7170.982.872
ReflectionResolution: 1.35→47.1 Å / Num. all: 144362 / Num. obs: 143557 / % possible obs: 99.4 % / Redundancy: 3.14 % / Biso Wilson estimate: 14.73 Å2 / Rmerge(I) obs: 0.044 / Χ2: 0.96 / Net I/σ(I): 12.2 / Scaling rejects: 3409
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsΧ2% possible all
1.35-1.43.10.4282.8446484455414456143501.0599.3
1.4-1.453.110.3613.2447124463514402143321.0399.5
1.45-1.523.110.2763.944741446191440814354199.6
1.52-1.63.10.2034.9449334477414452144250.9799.8
1.6-1.73.130.1526.1453204516414439144250.9299.9
1.7-1.833.160.1038.3459604572014481144660.8699.9
1.83-2.023.180.0711.7460584576614418143980.8199.9
2.02-2.313.190.04818.4462794586414399143710.8999.8
2.31-2.913.220.03824470654651314466144410.9799.8
2.91-47.13.10.02538.7447444344214441139951.1396.9

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97863.39-10.06
13 wavelength20.97845.05-8.13
13 wavelength30.96323.72-3.11
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se21.0540.190.0020.1340.623
2Se17.010.8570.3990.2780.533
3Se18.7740.7540.2340.1910.776
4Se16.2390.4320.0370.2330.524
5Se16.5210.3460.2090.3060.519
6Se25.490.7020.3940.0340.537
7Se18.8360.7870.30.0630.628
8Se28.330.1140.460.2490.631
9Se30.6410.540.3080.1320.328

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Processing

Software
NameVersionClassificationNB
d*TREK9.3Ddata scaling
SOLVE2.06phasing
REFMACrefmac_5.4.0034refinement
PDB_EXTRACT3.004data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.35→38.95 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.159 / SU B: 1.766 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FRIEDEL PAIRS WERE AVERAGED FOR REFINEMENT. RESIDUES 346-359, 428 (SIDE CHAIN), 429, 430 HAVE NO INTERPRETABLE ELECTRON DENSITY. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FRIEDEL PAIRS WERE AVERAGED FOR REFINEMENT. RESIDUES 346-359, 428 (SIDE CHAIN), 429, 430 HAVE NO INTERPRETABLE ELECTRON DENSITY. COORDINATES REPRESENT A HYPOTHETICAL MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 7201 9.8 %RANDOM
Rwork0.157 ---
obs0.16 73215 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.197 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.35→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 9 353 2795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222503
X-RAY DIFFRACTIONr_bond_other_d0.0010.021609
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9583421
X-RAY DIFFRACTIONr_angle_other_deg1.63633960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.315326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77926.05119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62215400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4551510
X-RAY DIFFRACTIONr_chiral_restr0.0070.02386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022866
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02468
X-RAY DIFFRACTIONr_mcbond_it1.6161.51590
X-RAY DIFFRACTIONr_mcbond_other0.8981.5645
X-RAY DIFFRACTIONr_mcangle_it2.45622564
X-RAY DIFFRACTIONr_scbond_it3.533913
X-RAY DIFFRACTIONr_scangle_it5.0184.5853
X-RAY DIFFRACTIONr_rigid_bond_restr1.59834112
X-RAY DIFFRACTIONr_sphericity_free7.7313354
X-RAY DIFFRACTIONr_sphericity_bonded5.23834061
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.35-1.3850.2555130.2248155438481597.977
1.385-1.4230.2465030.20647275269472799.26
1.423-1.4640.2574830.18646145127461499.415
1.464-1.5090.2175040.16944775004447799.54
1.509-1.5590.1944390.15943584815435899.626
1.559-1.6130.1764890.14141694669416999.764
1.613-1.6740.1944510.1440894546408999.868
1.674-1.7420.1894110.13439054320390599.907
1.742-1.820.1644300.132377542053775100
1.82-1.9080.1823780.13235983978359899.95
1.908-2.0110.1663910.133340737983407100
2.011-2.1330.1753530.12732503606325099.917
2.133-2.2790.1823260.13830603388306099.941
2.279-2.4610.1823210.142283631572836100
2.461-2.6950.1872940.151261829122618100
2.695-3.0120.2082800.16423772658237799.962
3.012-3.4740.22230.172210823312108100
3.474-4.2460.1722020.15917822001178299.15
4.246-5.970.2041300.17213731550137396.968
5.97-38.9540.288800.24367689467684.564

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