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- PDB-3ce8: Crystal structure of a duf3240 family protein (sbal_0098) from sh... -

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Basic information

Entry
Database: PDB / ID: 3ce8
TitleCrystal structure of a duf3240 family protein (sbal_0098) from shewanella baltica os155 at 2.40 A resolution
ComponentsPutative PII-like nitrogen regulatory protein
KeywordsUNKNOWN FUNCTION / Putative pii-like nitrogen regulatory protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Protein of unknown function DUF3240 / Protein of unknown function (DUF3240) / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DUF3240 domain-containing protein
Similarity search - Component
Biological speciesShewanella baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative PII-like nitrogen regulatory protein (YP_001048502.1) from Shewanella baltica OS155 at 2.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / 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 6, 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

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Assembly

Deposited unit
A: Putative PII-like nitrogen regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3455
Polymers14,0311
Non-polymers3144
Water1629
1
A: Putative PII-like nitrogen regulatory protein
hetero molecules

A: Putative PII-like nitrogen regulatory protein
hetero molecules

A: Putative PII-like nitrogen regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,03615
Polymers42,0943
Non-polymers94212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area6480 Å2
ΔGint-31.2 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.285, 71.285, 71.285
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-102-

PO4

21A-102-

PO4

31A-103-

PO4

DetailsAUTHORS STATE THAT THE CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A TRIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative PII-like nitrogen regulatory protein


Mass: 14031.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella baltica (bacteria) / Strain: OS155 / Gene: YP_001048502.1, Sbal_0098 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3CYS0
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 0.727M Ammonium dihydrogen phosphate, 0.114M Ammonium dihydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97926, 0.97879
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 3, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979261
30.978791
ReflectionResolution: 2.4→29.099 Å / Num. obs: 4934 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 68.285 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.467.40.6191.226813640.619100
2.46-2.537.50.4931.625293390.493100
2.53-2.67.40.3562.125333420.356100
2.6-2.687.30.3112.424493350.311100
2.68-2.777.40.252323403170.252100
2.77-2.877.30.2043.623023140.204100
2.87-2.987.30.149521812980.149100
2.98-3.17.40.1116.521792950.111100
3.1-3.247.40.0867.820082730.086100
3.24-3.397.20.0758.718892620.075100
3.39-3.587.20.0738.318702580.073100
3.58-3.797.20.0728.917922480.072100
3.79-4.067.20.0639.215852200.063100
4.06-4.387.10.0511.615562190.05100
4.38-4.87.10.05110.314132000.051100
4.8-5.3770.04811.912361760.048100
5.37-6.26.80.05211.810891590.052100
6.2-7.596.70.05410.39581430.054100
7.59-10.736.10.04912.56731100.04998.9
10.73-29.0995.30.04812329620.04890.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→29.099 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 16.971 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.314 / ESU R Free: 0.23
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. PO4 MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 5. EDO MOLECULES FROM THE CRYO SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 230 4.7 %RANDOM
Rwork0.196 ---
obs0.198 4920 99.82 %-
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: 23.205 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms710 0 18 9 737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022743
X-RAY DIFFRACTIONr_bond_other_d0.0020.02493
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9851003
X-RAY DIFFRACTIONr_angle_other_deg1.58231206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.832590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89724.84833
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93315128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.18153
X-RAY DIFFRACTIONr_chiral_restr0.0850.2113
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02802
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02144
X-RAY DIFFRACTIONr_mcbond_it1.2352450
X-RAY DIFFRACTIONr_mcbond_other0.1642182
X-RAY DIFFRACTIONr_mcangle_it2.6414724
X-RAY DIFFRACTIONr_scbond_it4.4366293
X-RAY DIFFRACTIONr_scangle_it6.4968278
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 14 -
Rwork0.327 349 -
all-363 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 22.821 Å / Origin y: 6.649 Å / Origin z: 48.58 Å
111213212223313233
T0.3568 Å20.0438 Å2-0.084 Å2-0.4462 Å20.0111 Å2--0.3701 Å2
L3.547 °20.3316 °2-0.6873 °2-7.1584 °22.6614 °2--6.9322 °2
S-0.2829 Å °0.5556 Å °0.0073 Å °-0.6405 Å °0.0807 Å °0.1361 Å °-0.3156 Å °-0.1198 Å °0.2021 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 4220 - 61
2X-RAY DIFFRACTION1AA54 - 10173 - 120

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