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- PDB-3g7p: Crystal structure of a nifx-associated protein of unknown functio... -

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Basic information

Entry
Database: PDB / ID: 3g7p
TitleCrystal structure of a nifx-associated protein of unknown function (afe_1514) from acidithiobacillus ferrooxidans atcc at 2.00 A resolution
ComponentsNitrogen fixation protein
KeywordsUNKNOWN FUNCTION / Duf 269 family protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyProtein of unknown function DUF269 / Uncharacterised protein family UPF0460 / Protein of unknown function, DUF269 / Putative cytoplasmic protein / Orthogonal Bundle / Mainly Alpha / Chem-PG6 / : / NifX-associated nitrogen fixation protein
Function and homology information
Biological speciesAcidithiobacillus ferrooxidans ATCC 23270 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NifX-associated protein of unknown function (YP_002425942.1) from Acidithiobacillus ferrooxidans ATCC 23270 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrogen fixation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9287
Polymers18,2501
Non-polymers6796
Water1,892105
1
A: Nitrogen fixation protein
hetero molecules

A: Nitrogen fixation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,85714
Polymers36,4992
Non-polymers1,35712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area1700 Å2
ΔGint-12.3 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.293, 49.293, 254.025
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Nitrogen fixation protein


Mass: 18249.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidithiobacillus ferrooxidans ATCC 23270 (bacteria)
Gene: Lferr_1232, YP_002425942.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: B5ER68, UniProt: B7JA91*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 22-363 OF THE FULL LENGTH PROTEIN.

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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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NANODROP, 0.20M Li2SO4, 30.0% PEG 4000, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 8, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979251
ReflectionResolution: 2→28.228 Å / Num. obs: 13459 / % possible obs: 100 % / Redundancy: 4.4 % / Biso Wilson estimate: 21.436 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 4.831
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.054.50.668143439620.668100
2.05-2.114.70.561.143029160.56100
2.11-2.174.60.4591.441809150.459100
2.17-2.244.60.4231.640918880.423100
2.24-2.314.60.3681.739768560.368100
2.31-2.394.50.2932.336988230.293100
2.39-2.484.50.2742.437318240.274100
2.48-2.584.60.2163.135597800.216100
2.58-2.74.60.1793.834237470.179100
2.7-2.834.50.1544.232687220.154100
2.83-2.984.50.1524.531256890.152100
2.98-3.164.40.116.129676670.11100
3.16-3.384.40.092727036110.092100
3.38-3.654.40.0768.626055930.076100
3.65-44.30.0689.523645470.068100
4-4.474.20.05811.222145220.058100
4.47-5.164.10.05412.318094440.054100
5.16-6.323.90.06210.516184100.062100
6.32-8.943.60.0610.111923270.06100
8.94-28.22830.04410.86452160.04497

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→28.228 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.141 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.163
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ETHYLENE GLYCOL (EDO), A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE. 5. SULFATE MOLECULES (SO4), AND POLYETHYLENE GLYCOL (PG6) FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 659 4.9 %RANDOM
Rwork0.204 ---
obs0.206 13359 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 78.62 Å2 / Biso mean: 40.886 Å2 / Biso min: 20.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.19 Å20 Å2
2--0.37 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2→28.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 41 105 1302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221230
X-RAY DIFFRACTIONr_bond_other_d0.0040.02877
X-RAY DIFFRACTIONr_angle_refined_deg1.5482.0041652
X-RAY DIFFRACTIONr_angle_other_deg0.8932122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2465146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.11323.09155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47615215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9421511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021316
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02252
X-RAY DIFFRACTIONr_nbd_refined0.2280.3250
X-RAY DIFFRACTIONr_nbd_other0.1960.3886
X-RAY DIFFRACTIONr_nbtor_refined0.1870.5596
X-RAY DIFFRACTIONr_nbtor_other0.0940.5598
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.5121
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.352
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.510
X-RAY DIFFRACTIONr_mcbond_it1.5492779
X-RAY DIFFRACTIONr_mcbond_other0.2312292
X-RAY DIFFRACTIONr_mcangle_it2.03441167
X-RAY DIFFRACTIONr_scbond_it4.4246555
X-RAY DIFFRACTIONr_scangle_it5.1468484
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 48 -
Rwork0.244 910 -
all-958 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -7.9983 Å / Origin y: 15.792 Å / Origin z: -9.1465 Å
111213212223313233
T-0.2125 Å2-0.0085 Å20.0218 Å2--0.1788 Å2-0.0364 Å2---0.1933 Å2
L3.9557 °2-0.4876 °22.0958 °2-1.1441 °2-0.4513 °2--2.8802 °2
S0.0041 Å °0.3258 Å °-0.079 Å °-0.0864 Å °-0.0825 Å °-0.1411 Å °0.0112 Å °0.2414 Å °0.0784 Å °

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