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- PDB-2fup: Crystal structure of a putative flagella synthesis protein flgn (... -

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Basic information

Entry
Database: PDB / ID: 2fup
TitleCrystal structure of a putative flagella synthesis protein flgn (pa3352) from pseudomonas aeruginosa at 1.48 A resolution
Componentshypothetical protein PA3352Hypothesis
KeywordsBIOSYNTHETIC PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


bacterial-type flagellum assembly
Similarity search - Function
FlgN-like / FlgN-like protein / FlgN-like superfamily / FlgN protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.48 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_252042.1) from Pseudomonas aeruginosa at 1.48 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PA3352
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5452
Polymers17,4271
Non-polymers1181
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.531, 62.531, 80.241
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein hypothetical protein PA3352 / Hypothesis


Mass: 17427.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: np_252042.1 / Production host: Escherichia coli (E. coli) / References: GenBank: 15598548, UniProt: Q9HYP4*PLUS
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.24965 Å3/Da / Density % sol: 45.324837 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4
Details: 20.0% MPD, 0.1M Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9797, 0.9999, 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.99991
30.97951
ReflectionResolution: 1.48→29.74 Å / Num. obs: 27261 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value% possible all
1.48-1.565.20.764138500.764100
1.56-1.657.10.5171.437050.517100
1.65-1.777.20.3382.234870.338100
1.77-1.917.20.2183.432610.218100
1.91-2.097.20.1235.930290.123100
2.09-2.347.20.0768.727350.076100
2.34-2.77.10.0669.524430.066100
2.7-3.3170.0619.420990.061100
3.31-4.686.90.04810.816570.048100
4.68-29.746.30.03812.69950.03899.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.48→29.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.39 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.068
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. RESIDUES 115-116 WERE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1361 5 %RANDOM
Rwork0.188 ---
obs0.19 27190 99.94 %-
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 mean: 22.417 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2---0.51 Å20 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.48→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 8 110 1092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211018
X-RAY DIFFRACTIONr_bond_other_d0.0010.02971
X-RAY DIFFRACTIONr_angle_refined_deg1.7132.0011372
X-RAY DIFFRACTIONr_angle_other_deg0.92332245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2465130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34724.82156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3615189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9911512
X-RAY DIFFRACTIONr_chiral_restr0.0990.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02190
X-RAY DIFFRACTIONr_nbd_refined0.2470.2270
X-RAY DIFFRACTIONr_nbd_other0.1870.21008
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2514
X-RAY DIFFRACTIONr_nbtor_other0.0840.2626
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.29
X-RAY DIFFRACTIONr_mcbond_it2.4583664
X-RAY DIFFRACTIONr_mcbond_other0.5523266
X-RAY DIFFRACTIONr_mcangle_it3.11551008
X-RAY DIFFRACTIONr_scbond_it5.3528384
X-RAY DIFFRACTIONr_scangle_it8.11811362
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 105 -
Rwork0.279 1871 -
all-1976 -
obs--99.65 %
Refinement TLS params.Method: refined / Origin x: 37.879 Å / Origin y: 52.12 Å / Origin z: 28.218 Å
111213212223313233
T-0.0593 Å2-0.0069 Å20.0041 Å2--0.0807 Å20.0008 Å2---0.1362 Å2
L0.9437 °2-0.8921 °2-0.0404 °2-1.2366 °20.2283 °2--0.5634 °2
S0.0088 Å °0.0807 Å °-0.1659 Å °0.0089 Å °-0.0655 Å °0.2043 Å °0.0884 Å °-0.0151 Å °0.0567 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDAuth seq-IDLabel seq-ID
11 - 1142 - 115
2117 - 130118 - 131

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