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- PDB-3u24: The structure of a putative lipoprotein of unknown function from ... -

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Basic information

Entry
Database: PDB / ID: 3u24
TitleThe structure of a putative lipoprotein of unknown function from Shewanella oneidensis.
Componentsputative Lipoprotein
KeywordsLIPID BINDING PROTEIN / COG4805 / DUF885 / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / putative lipoprotein
Function / homologyProtein of unknown function DUF885 / Bacterial protein of unknown function (DUF885) / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / ACETIC ACID / IMIDAZOLE / DUF885 family lipoprotein
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsCuff, M.E. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of a putative lipoprotein of unknown function from Shewanella oneidensis.
Authors: Cuff, M.E. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A.
History
DepositionSep 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Oct 16, 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 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: putative Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,90526
Polymers66,3871
Non-polymers1,51725
Water6,846380
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.427, 96.427, 133.947
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-975-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein putative Lipoprotein


Mass: 66387.359 Da / Num. of mol.: 1 / Fragment: residues 21-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_2570 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q8EE20

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Non-polymers , 6 types, 405 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M zinc acetate, 0.1M imidazole pH 8, 20% PEG 3000, 10% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 24, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionRedundancy: 9.2 % / Av σ(I) over netI: 26.23 / Number: 320044 / Rmerge(I) obs: 0.101 / Χ2: 1.41 / D res high: 2.25 Å / D res low: 50 Å / Num. obs: 34837 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.15099.310.0683.5938.7
4.856.110010.072.3729.5
4.234.8510010.0591.9269.7
3.854.2310010.0621.8359.8
3.573.8510010.071.7629.7
3.363.5710010.0811.5989.6
3.193.3610010.0921.4419.5
3.053.1910010.1141.2839.4
2.943.0510010.1321.2029.3
2.832.9410010.1531.1259.2
2.752.8310010.1741.0259.2
2.672.7599.910.1991.0299.2
2.62.6799.910.241.0089.2
2.532.699.910.2780.989.2
2.482.5399.810.2790.929.2
2.422.4899.910.3080.949.2
2.382.4299.910.3530.9369.1
2.332.3810010.3960.9049.1
2.292.3399.810.4360.9798.3
2.252.2910010.4741.0137.6
ReflectionResolution: 2.25→50 Å / Num. all: 34837 / Num. obs: 34837 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.25-2.297.60.4741100
2.29-2.338.30.436199.8
2.33-2.389.10.3961100
2.38-2.429.10.353199.9
2.42-2.489.20.308199.9
2.48-2.539.20.279199.8
2.53-2.69.20.278199.9
2.6-2.679.20.24199.9
2.67-2.759.20.199199.9
2.75-2.839.20.1741100
2.83-2.949.20.1531100
2.94-3.059.30.1321100
3.05-3.199.40.1141100
3.19-3.369.50.0921100
3.36-3.579.60.0811100
3.57-3.859.70.071100
3.85-4.239.80.0621100
4.23-4.859.70.0591100
4.85-6.19.50.071100
6.1-508.70.068199.3

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.25 Å / D res low: 50 Å / FOM : 0.264 / FOM acentric: 0.292 / FOM centric: 0 / Reflection: 34738 / Reflection acentric: 31329 / Reflection centric: 3409
Phasing MAD setR cullis acentric: 1.99 / R cullis centric: 1 / Highest resolution: 2.25 Å / Lowest resolution: 50 Å / Loc acentric: 0.2 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 31329 / Reflection centric: 3409
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
13.69-501.480.50.39577
7.93-13.691.170.50.3519177
5.58-7.932.040.50.21278278
4.31-5.581.370.40.22363386
3.51-4.311.380.30.23789472
2.96-3.511.930.20.15559585
2.56-2.962.950.20.17657665
2.25-2.563.370.1010069769
Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

IDB isoFract xFract yFract zOccupancy
134.91790.4640.0160.073.793
230.53040.311-0.03-0.0273.194
327.60520.502-0.0880.283.125
430.73570.487-0.2630.0932.909
530.56010.329-0.0130.0052.78
625.36490.104-0.1970.0463.013
736.43720.123-0.3480.1153.211
824.70690.185-0.112-0.0322.878
971.69380.105-0.204-0.023.195
1034.51440.413-0.1010.0372.805
1155.81560.033-0.3850.0392.922
1228.6350.14-0.3080.0652.409
1330.58140.304-0.1460.1392.648
1433.40210.144-0.2510.142.154
1525.90770.303-0.187-0.0011.782
1643.96580.052-0.285-0.1051.467
1736.1270.5650.0140.1291.324
1835.30840.531-0.0780.151.346
1952.51590.282-0.2360.2691.363
2099.71990.6610.1470.0961.633
2130.6340.153-0.104-0.080.731
2248.9280.327-0.049-0.0180.505
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
13.69-500.2430.43901729577
7.93-13.690.4010.5380696519177
5.58-7.930.4410.536015561278278
4.31-5.580.4290.5027492363386
3.51-4.310.4050.456042613789472
2.96-3.510.3290.364061445559585
2.56-2.960.2210.24083227657665
2.25-2.560.1280.13701083810069769
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 34738
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.5-100680.547518
7.5-9.565.30.872505
6.39-7.560.60.848606
5.66-6.3964.50.873695
5.13-5.6659.80.896774
4.73-5.13600.914830
4.41-4.7360.80.92895
4.15-4.4161.50.922950
3.93-4.1560.50.92993
3.74-3.9360.60.9271047
3.57-3.74600.9131107
3.43-3.5760.70.9161127
3.3-3.4365.20.9051182
3.19-3.3630.9091238
3.08-3.1965.50.9011287
2.99-3.0864.60.8951313
2.9-2.9965.20.8961326
2.82-2.967.40.91368
2.75-2.8270.90.9111436
2.68-2.7570.60.9091449
2.62-2.6872.70.9031498
2.56-2.6272.10.9011554
2.51-2.56740.9111539
2.46-2.51760.9161593
2.41-2.46760.911588
2.36-2.4177.20.9091647
2.32-2.3679.40.9041674
2.25-2.3280.20.872999

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.25→39.37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.287 / SU ML: 0.121 / SU R Cruickshank DPI: 0.2237 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.177
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20045 1747 5 %RANDOM
Rwork0.1621 ---
obs0.16409 33008 99.9 %-
all-34755 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.158 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.25→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4412 0 59 380 4851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024593
X-RAY DIFFRACTIONr_bond_other_d0.0010.023130
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9526205
X-RAY DIFFRACTIONr_angle_other_deg0.94337611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2715552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72324.558226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74415797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4131524
X-RAY DIFFRACTIONr_chiral_restr0.0870.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025120
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02962
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 103 -
Rwork0.192 2256 -
obs--100 %
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)
10.5112-0.1162-0.05960.3762-0.05580.34440.0581-0.0181-0.01620.0288-0.0674-0.07330.0330.03050.00930.1272-0.0654-0.02360.07080.0180.09287.207753.85516.5653
20.90970.13840.39390.68340.21981.52940.0096-0.04330.0486-0.1521-0.00470.08330.0366-0.3324-0.00490.1055-0.0560.00010.10230.01290.1003-28.022370.2795-5.9462
34.038-0.8580.00340.2642-0.27170.9258-0.11040.678-0.29720.0316-0.1148-0.00490.0117-0.00820.22520.1309-0.04280.02240.1721-0.08350.1055-3.478368.082-13.1143
40.6790.16280.51390.13530.13240.5934-0.02990.02880.060.00080.02170.0241-0.0159-0.04790.00820.1516-0.07070.02750.05950.00620.1261-14.724271.8874-2.4485
50.92930.10030.06551.4584-0.30980.3960.0919-0.13820.10820.0002-0.07630.069-0.0414-0.0499-0.01560.1464-0.07510.01590.0713-0.02840.0873-12.961469.203510.1803
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 294
2X-RAY DIFFRACTION2A295 - 359
3X-RAY DIFFRACTION3A360 - 404
4X-RAY DIFFRACTION4A405 - 486
5X-RAY DIFFRACTION5A487 - 591

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