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- PDB-3buu: Crystal structure of LolA superfamily protein NE2245 from Nitroso... -

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Basic information

Entry
Database: PDB / ID: 3buu
TitleCrystal structure of LolA superfamily protein NE2245 from Nitrosomonas europaea
ComponentsUncharacterized LolA superfamily protein NE2245
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / LolA superfamily / Nitrosomonas europaea / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Uncharacterised conserved protein UCP028205 / : / Putative outer membrane lipoprotein-sorting protein / Outer membrane lipoprotein-sorting protein / Lipoprotein localisation LolA/LolB/LppX / outer membrane lipoprotein receptor (LolB), chain A / Lipoprotein localisation LolA/LolB/LppX / Clam / Mainly Beta
Similarity search - Domain/homology
Outer membrane lipoprotein-sorting protein
Similarity search - Component
Biological speciesNitrosomonas europaea ATCC 19718 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsChang, C. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of LolA superfamily protein NE2245 from Nitrosomonas europaea.
Authors: Chang, C. / Wu, R. / Clancy, S. / Joachimiak, A.
History
DepositionJan 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized LolA superfamily protein NE2245
B: Uncharacterized LolA superfamily protein NE2245


Theoretical massNumber of molelcules
Total (without water)53,0802
Polymers53,0802
Non-polymers00
Water8,089449
1
A: Uncharacterized LolA superfamily protein NE2245


Theoretical massNumber of molelcules
Total (without water)26,5401
Polymers26,5401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized LolA superfamily protein NE2245


Theoretical massNumber of molelcules
Total (without water)26,5401
Polymers26,5401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.019, 59.116, 89.676
Angle α, β, γ (deg.)90.00, 90.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized LolA superfamily protein NE2245


Mass: 26540.008 Da / Num. of mol.: 2 / Fragment: Residues 32-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea ATCC 19718 (bacteria)
Species: Nitrosomonas europaea / Strain: IFO 14298 / Gene: NE2245 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q82SR2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 1.75 Å3/Da / Density % sol: 29.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 25% PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2007
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 114457 / Num. obs: 112699 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 47.67
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 6.84 / Num. unique all: 10959 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→49.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.303 / SU ML: 0.028 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19227 5639 5 %RANDOM
Rwork0.15834 ---
all0.16004 112526 --
obs0.16004 112526 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.385 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.08 Å2
2--0.08 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.2→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4013 0 0 449 4462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224140
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9685686
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40224215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74715770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9891541
X-RAY DIFFRACTIONr_chiral_restr0.1120.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023303
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.21861
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22910
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2411
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.2172
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.280
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0991.52569
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.78624122
X-RAY DIFFRACTIONr_scbond_it4.07631774
X-RAY DIFFRACTIONr_scangle_it5.4724.51541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 395 -
Rwork0.169 7523 -
obs-7918 94.27 %
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)
10.08690.0501-0.03320.158-0.02580.1679-0.0008-0.012200.0019-0.0028-0.00360.0056-0.0030.0036-0.00880.00090.00010.00010.0005-0.006931.065127.624239.3614
20.0786-0.0574-0.07970.04780.09340.28950.0022-0.0072-0.0028-0.02870.0043-0.0028-0.02630.0272-0.0065-0.0009-0.00430.0007-0.00080.0014-0.004440.499627.983719.6845
30.31250.2109-0.1631.3420.59560.5887-0.0196-0.02780.001-0.02370.0322-0.0291-0.00930.0229-0.0126-0.0108-0.00060.00070.00230.0007-0.007242.744227.825930.441
40.2733-0.2659-0.05320.38520.01940.1441-0.0246-0.01750.01110.02520.0198-0.0113-0.0048-0.00680.0048-0.00760.0003-0.002-0.0072-0.0009-0.003748.818357.40985.1057
50.35850.09880.09820.17280.24170.3434-0.0788-0.06280.05030.17130.0599-0.03780.05790.03310.01890.0570.0331-0.02840.001-0.0016-0.013258.312358.755623.8708
61.2982-0.9621-0.41192.86771.29671.1405-0.1228-0.09620.06680.1270.1447-0.10130.0480.0475-0.0219-0.00320.0129-0.0181-0.0001-0.01-0.008660.53357.936313.9217
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA35 - 517 - 23
2X-RAY DIFFRACTION1AA137 - 241109 - 213
3X-RAY DIFFRACTION2AA52 - 11924 - 91
4X-RAY DIFFRACTION2AA242 - 257214 - 229
5X-RAY DIFFRACTION3AA120 - 13692 - 108
6X-RAY DIFFRACTION4BB35 - 517 - 23
7X-RAY DIFFRACTION4BB137 - 241109 - 213
8X-RAY DIFFRACTION5BB52 - 11924 - 91
9X-RAY DIFFRACTION5BB242 - 253214 - 225
10X-RAY DIFFRACTION6BB120 - 13692 - 108

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