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- PDB-3erm: The crystal structure of a conserved protein with unknown functio... -

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Basic information

Entry
Database: PDB / ID: 3erm
TitleThe crystal structure of a conserved protein with unknown function from Pseudomonas syringae pv. tomato str. DC3000
Componentsuncharacterized conserved protein
Keywordsstructural genomics / unknown function / APC85034 / PPSPTO1197 / seudomonas syringae pv. tomato str. DC3000 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyPSPTO_1197 like / Uncharacterised protein family YebG / YebG-like superfamily / YebG protein / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / YebG family protein
Function and homology information
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å
AuthorsTan, K. / Zhou, M. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a conserved protein with unknown function from Pseudomonas syringae pv. tomato str. DC3000
Authors: Tan, K. / Zhou, M. / Clancy, S. / Joachimiak, A.
History
DepositionOct 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized conserved protein
B: uncharacterized conserved protein
C: uncharacterized conserved protein
D: uncharacterized conserved protein
E: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6406
Polymers50,5445
Non-polymers961
Water23413
1
A: uncharacterized conserved protein
B: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3143
Polymers20,2182
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-33 kcal/mol
Surface area8020 Å2
MethodPISA
2
C: uncharacterized conserved protein

C: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)20,2182
Polymers20,2182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area2660 Å2
ΔGint-24 kcal/mol
Surface area7770 Å2
MethodPISA
3
D: uncharacterized conserved protein

D: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)20,2182
Polymers20,2182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area2890 Å2
ΔGint-26 kcal/mol
Surface area7920 Å2
MethodPISA
4
E: uncharacterized conserved protein

E: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)20,2182
Polymers20,2182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2670 Å2
ΔGint-22 kcal/mol
Surface area6380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.971, 74.971, 213.784
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsExperimentally unknown. It is predicted that the chains A and B forms a dimer. The chains C and D forms dimers with their symmetry-related molecules by the same operator x+1, x-y+1, -z+1/6, respectively. The chain E forms a dimer with its symmetry related molecule by an operator x-y+1, -y, -z.

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Components

#1: Protein
uncharacterized conserved protein


Mass: 10108.802 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: str. DC3000
Gene: Pseudomonas syringae pv. tomato, PSPTO1197, PSPTO_1197
Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q887T9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1M Bicine, 2.4M Ammonium Sulfate, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937, 0.97948
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2007 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
20.979481
ReflectionResolution: 2.45→42 Å / Num. all: 13874 / Num. obs: 13874 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 43.6
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 1.96 / Num. unique all: 666 / % possible all: 98.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.45→41.27 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 25.429 / SU ML: 0.25 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.462 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26892 690 5 %RANDOM
Rwork0.2141 ---
all0.2168 13080 --
obs0.2168 13080 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.064 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.35 Å20 Å2
2--0.69 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.45→41.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 5 13 2444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222463
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9753325
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9815315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.1826.161112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.42415447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.135159
X-RAY DIFFRACTIONr_chiral_restr0.1120.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021811
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.19821590
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.08332517
X-RAY DIFFRACTIONr_scbond_it1.4132873
X-RAY DIFFRACTIONr_scangle_it2.2713807
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 59 -
Rwork0.253 897 -
obs-749 96.86 %
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)
12.2681.1281-0.676810.9556-0.77072.3502-0.023-0.10810.40520.58130.076-0.1646-0.41950.2559-0.05310.149-0.0076-0.06770.0764-0.0050.30174.37123.64327.603
27.0326-2.43341.67336.7970.16026.1166-0.09310.26940.1959-0.3139-0.05690.0648-0.40910.27480.150.1753-0.0137-0.02050.019-0.00530.374168.84317.58217.973
35.19662.0234-0.56748.8392-0.22496.53710.24770.51310.3669-0.19330.1808-0.51590.08150.2572-0.42850.0945-0.01380.03790.2157-0.00790.648980.52141.30113.753
48.9172-2.37391.37566.2486-2.00647.12930.239-0.7517-0.41480.33150.4460.99160.1988-0.7866-0.68490.1313-0.03440.00270.16460.12340.681747.47525.32523.606
56.5834-2.1520.14176.41351.76224.25680.05390.2957-0.028-0.0683-0.36230.6514-0.1546-0.60840.30840.04980.0138-0.0070.1156-0.06140.452564.1773.432.908
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 84
2X-RAY DIFFRACTION2B19 - 82
3X-RAY DIFFRACTION3C19 - 82
4X-RAY DIFFRACTION4D19 - 83
5X-RAY DIFFRACTION5E24 - 81

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