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Basic information

Entry
Database: PDB / ID: 2iiu
TitleCrystal structure of a putative PhoU-like phosphate regulatory protein (NP_719307.1) from Shewanella oneidensis MR-1 at 2.28 A resolution.
ComponentsHypothetical protein
KeywordsStructural Genomics/Unknown function / NP_719307.1 / conserved hypothetical protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / Structural Genomics-Unknown function COMPLEX
Function / homologyProtein of unknown function DUF47 / Putative phosphate transport regulator / Protein of unknown function DUF47 / Phosphate transport system protein phou homolog 2; domain 2 / PhoU-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / TIGR00153 family protein
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.28 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of conserved hypothetical protein (NP_719307.1) from Shewanella Oneidensis MR-1 at 2.28 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 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 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9007
Polymers77,6523
Non-polymers2484
Water3,657203
1
A: Hypothetical protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)156,42124
Polymers155,3046
Non-polymers1,11718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
MethodPQS
2
B: Hypothetical protein
C: Hypothetical protein
hetero molecules

B: Hypothetical protein
C: Hypothetical protein
hetero molecules

B: Hypothetical protein
C: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,4909
Polymers155,3046
Non-polymers1863
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
3
A: Hypothetical protein
hetero molecules
x 6
B: Hypothetical protein
C: Hypothetical protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)467,40242
Polymers465,91218
Non-polymers1,49024
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
crystal symmetry operation10_445y-1/3,x-2/3,-z+1/31
crystal symmetry operation11_455x-y-1/3,-y+1/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
crystal symmetry operation13_444x-2/3,y-1/3,z-1/31
crystal symmetry operation14_544-y+1/3,x-y-1/3,z-1/31
crystal symmetry operation15_554-x+y+1/3,-x+2/3,z-1/31
Buried area47020 Å2
ΔGint-132 kcal/mol
Surface area154620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.880, 99.880, 397.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERLEUAA13 - 7014 - 71
21SERLEUBB13 - 7014 - 71
31SERLEUCC13 - 7014 - 71
42VALLEUAA80 - 14581 - 146
52VALLEUBB80 - 14581 - 146
62VALLEUCC80 - 14581 - 146
73ARGVALAA151 - 226152 - 227
83ARGVALBB151 - 226152 - 227
93ARGVALCC151 - 226152 - 227
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Hypothetical protein /


Mass: 25884.010 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: NP_719307.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EAX1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.7 Å3/Da / Density % sol: 54.08 %
Description: X-RAY DATA WERE COLLECTED TO A MAXIMUM RESOLUTION OF 2.00 ANGSTROMS BUT DUE TO HEAVY ICE RINGS BEYOND 2.27 ANGSTROMS, ONLY REFLECTIONS BETWEEN 47 AND 2.28 ANGSTROMS WERE USED FOR THE REFINEMENT.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5
Details: 1.0M NaCitrate, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.918370, 0.979318, 0.979035
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 7, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.9793181
30.9790351
ReflectionResolution: 2→46.73 Å / Num. obs: 52278 / % possible obs: 98.5 % / Redundancy: 20.2 % / Biso Wilson estimate: 39.053 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 14.54
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
2-2.050.6512.91515921100
2.05-2.140.6033.63897531100
2.14-2.250.3914.2683704194.4
2.25-2.390.5645.55117277193.2
2.39-2.580.4219.071497001100
2.58-2.840.26513.571448601100
2.84-3.250.16119.651442361100
3.25-4.080.09828.78139178199.5
4.08-47.50.08337.22139362199.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHARPphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.28→47.458 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.387 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.222
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. ELECTRON DENSITY FOR RESIDUES 1-12 ON THE A AND B SUBUNITS AND FOR RESIDUES 1-6 ON THE C SUBUNIT ARE DISORDERED, THEREFORE THESE RESIDUES WERE NOT MODELED. 5. ELECTRON DENSITIES FOR THE FOLLOWING REGIONS ARE DISORDERD: A72-A74, A148-A150,B73,B148-B150,C73-C76, AND C149-C150; THEREFORE THESE RESIDUES WERE NOT MODELED. 6. ETHYLENE GLYCOL MOLECULES USED AS A CRYOPROTECTANT HAVE BEEN INCORPORATED INTO THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1812 5.1 %RANDOM
Rwork0.2 ---
obs0.202 35397 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.494 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å21.22 Å20 Å2
2--2.44 Å20 Å2
3----3.66 Å2
Refinement stepCycle: LAST / Resolution: 2.28→47.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4799 0 16 203 5018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224899
X-RAY DIFFRACTIONr_bond_other_d0.0020.024690
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9816624
X-RAY DIFFRACTIONr_angle_other_deg0.88310798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8785627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54125.15200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59415869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9691533
X-RAY DIFFRACTIONr_chiral_restr0.0880.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025385
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02905
X-RAY DIFFRACTIONr_nbd_refined0.2280.31242
X-RAY DIFFRACTIONr_nbd_other0.1590.34594
X-RAY DIFFRACTIONr_nbtor_refined0.1840.52488
X-RAY DIFFRACTIONr_nbtor_other0.0910.52819
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.5292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.3120
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.521
X-RAY DIFFRACTIONr_mcbond_it1.82633257
X-RAY DIFFRACTIONr_mcbond_other0.37231282
X-RAY DIFFRACTIONr_mcangle_it2.85855059
X-RAY DIFFRACTIONr_scbond_it5.24271846
X-RAY DIFFRACTIONr_scangle_it7.44991565
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1166TIGHT POSITIONAL0.060.05
2B1166TIGHT POSITIONAL0.060.05
3C1166TIGHT POSITIONAL0.070.05
1A1737LOOSE POSITIONAL0.495
2B1737LOOSE POSITIONAL0.445
3C1737LOOSE POSITIONAL0.435
1A1166TIGHT THERMAL0.170.5
2B1166TIGHT THERMAL0.160.5
3C1166TIGHT THERMAL0.140.5
1A1737LOOSE THERMAL2.210
2B1737LOOSE THERMAL2.1310
3C1737LOOSE THERMAL2.1510
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 138 -
Rwork0.225 2438 -
obs-2576 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)
11.87740.04670.47451.91670.16854.626-0.09670.12810.0783-0.0143-0.00940.0513-0.60130.17870.1061-0.1535-0.0485-0.0351-0.33070.022-0.14424.331717.70727.9603
20.90590.1165-0.01050.97680.52953.8538-0.03780.02840.0341-0.01640.0137-0.0862-0.05910.59880.0241-0.2217-0.0262-0.0216-0.15920.0286-0.145214.18846.537631.4983
31.84370.33711.66390.93580.82126.7807-0.1465-0.43630.190.1759-0.06090.1613-0.251-0.92410.2074-0.1962-0.0028-0.0008-0.0008-0.0569-0.022931.718827.6573-12.9777
41.4183-0.05330.0681.27920.12075.288-0.0358-0.1325-0.20250.09250.00410.07660.7079-0.20630.0318-0.1492-0.05640.0053-0.1506-0.03960.012441.073916.2103-16.8858
51.16880.64291.92341.90810.20344.8155-0.0433-0.1694-0.2342-0.1274-0.0999-0.06711.055-0.87690.14320.0388-0.21890.00160.1697-0.0125-0.049135.932915.923541.327
60.1633-0.15760.62361.05380.83147.9355-0.0380.06370.0283-0.1486-0.13840.1463-0.4611-1.41540.1764-0.08130.0261-0.02880.3372-0.0313-0.105134.441530.903245.6803
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA13 - 11314 - 114
22AA114 - 226115 - 227
33BB13 - 11314 - 114
44BB114 - 226115 - 227
55CC7 - 1138 - 114
66CC114 - 226115 - 227

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