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- PDB-3k4i: CRYSTAL STRUCTURE OF uncharacterized protein PSPTO_3204 from Pseu... -

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Basic information

Entry
Database: PDB / ID: 3k4i
TitleCRYSTAL STRUCTURE OF uncharacterized protein PSPTO_3204 from Pseudomonas syringae pv. tomato str. DC3000
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


4-hydroxy-4-methyl-2-oxoglutarate aldolase / 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3070 / Ribonuclease E inhibitor RraA/RraA-like / Ribonuclease E inhibitor RraA/RraA-like protein / Ribonuclease E inhibitor RraA/RraA-like superfamily / Aldolase/RraA / Glucose Oxidase; domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 3-Layer(bba) Sandwich / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-hydroxy-4-methyl-2-oxoglutarate aldolase
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.69 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF uncharacterized protein PSPTO_3204 from Pseudomonas syringae pv. tomato str. DC3000
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 24, 2012Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,8149
Polymers79,6353
Non-polymers1796
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-81 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.442, 124.857, 66.912
Angle α, β, γ (deg.)90.000, 97.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein uncharacterized protein


Mass: 26544.949 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: AAO56687.1, PSPTO3204 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q880F6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M MgCl2, 0.1 M Bis-Tris, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 118996 / % possible obs: 96.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.104 / Χ2: 3.06 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.69-1.722.70.56954701.138186.6
1.72-1.752.80.52756351.219194
1.75-1.782.90.50957991.288194.7
1.78-1.8230.44758541.32194.5
1.82-1.8630.37758971.412196.8
1.86-1.930.33659481.62196.2
1.9-1.953.10.27958641.66197.2
1.95-23.10.24859891.774196.8
2-2.063.10.21359691.997197.9
2.06-2.133.10.19160202.123197.7
2.13-2.213.10.16659782.217197.7
2.21-2.293.10.15360352.459197.7
2.29-2.43.10.13760272.492198.6
2.4-2.523.10.12459732.835198.1
2.52-2.683.10.1160953.102198
2.68-2.893.10.09960443.743198.6
2.89-3.183.10.09860975.723199.3
3.18-3.643.20.08960706.993199.9
3.64-4.593.10.06961007.24199.2
4.59-503.20.05861326.766199.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0089refinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.69→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.867 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2985 5.1 %RANDOM
Rwork0.178 ---
obs0.18 58815 94.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 57.01 Å2 / Biso mean: 14.076 Å2 / Biso min: 2.13 Å2
Baniso -1Baniso -2Baniso -3
1-11.44 Å20 Å25.75 Å2
2---4.98 Å20 Å2
3----6.46 Å2
Refinement stepCycle: LAST / Resolution: 1.69→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 6 374 4964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224660
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.966342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7435613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10524.67197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22215758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3871533
X-RAY DIFFRACTIONr_chiral_restr0.0920.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213507
X-RAY DIFFRACTIONr_mcbond_it1.0263.53049
X-RAY DIFFRACTIONr_mcangle_it2.883504941
X-RAY DIFFRACTIONr_scbond_it5.949501611
X-RAY DIFFRACTIONr_scangle_it1.4034.51399
LS refinement shellResolution: 1.693→1.736 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 191 -
Rwork0.242 3445 -
all-3636 -
obs--79.63 %
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)
10.26470.0804-0.01850.28050.20030.84820.0196-0.0155-0.0310.01130.0093-0.0005-0.0676-0.0077-0.02890.01640.0063-0.02610.11470.00850.11423.118764.956860.3959
20.19120.1621-0.04320.5984-0.53550.95790.002-0.02620.02250.0444-0.0555-0.0234-0.07030.07440.05360.0254-0.0012-0.00570.05770.00050.116932.254190.048944.9821
30.37290.2024-0.18150.3999-0.27920.52830.00690.04230.0030.00050.01130.0144-0.0296-0.0216-0.01820.01360.0058-0.03560.1206-0.00630.121221.276665.105929.382
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 218
2X-RAY DIFFRACTION1A501 - 502
3X-RAY DIFFRACTION1A245 - 398
4X-RAY DIFFRACTION2B9 - 218
5X-RAY DIFFRACTION2B501 - 502
6X-RAY DIFFRACTION2B245 - 404
7X-RAY DIFFRACTION3C2 - 220
8X-RAY DIFFRACTION3C501 - 502
9X-RAY DIFFRACTION3C245 - 403

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