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- PDB-3mdk: Structure of stringent starvation protein A (sspA) from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 3mdk
TitleStructure of stringent starvation protein A (sspA) from Pseudomonas putida
ComponentsStringent starvation protein A
Keywordstranscriptional regulator / structural genomics / GST-superfamily / sspA / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Stringent starvation protein A, N-terminal / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Stringent starvation protein A, N-terminal / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Stringent starvation protein A
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of stringent starvation protein A (sspA) from Pseudomonas putida
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionMar 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stringent starvation protein A
B: Stringent starvation protein A


Theoretical massNumber of molelcules
Total (without water)50,2802
Polymers50,2802
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-12 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.060, 48.916, 91.388
Angle α, β, γ (deg.)90.000, 107.240, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Stringent starvation protein A


Mass: 25139.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: PP1320, sspA / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q88N92
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 25% PEG 3350, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 38147 / % possible obs: 97.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.077 / Χ2: 1.678 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.885.40.49919100.854197.7
1.88-1.925.60.44319130.9198.1
1.92-1.955.90.36819210.929198.5
1.95-1.9960.30919150.953198.5
1.99-2.0460.25919371.083198.4
2.04-2.086.10.21918781.098198
2.08-2.146.10.17519271.194198.3
2.14-2.196.10.15119171.299198.3
2.19-2.266.10.14119211.295198.5
2.26-2.3360.11619211.44198.5
2.33-2.416.10.10419191.606199
2.41-2.516.10.09919311.718198.7
2.51-2.636.10.08819701.929199.2
2.63-2.766.10.08219462.124199.8
2.76-2.946.10.07619662.199199.7
2.94-3.1660.07119472.371199.4
3.16-3.485.70.06919312.41196.9
3.48-3.995.40.06517932.582190.8
3.99-5.0250.06216982.957185.6
5.02-505.20.06318863.226191.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
SHELXEmodel building
SHELXDphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.271 / WRfactor Rwork: 0.228 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.81 / SU B: 8.892 / SU ML: 0.12 / SU R Cruickshank DPI: 0.157 / SU Rfree: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1925 5.1 %RANDOM
Rwork0.216 ---
obs0.218 38081 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.42 Å2 / Biso mean: 21.426 Å2 / Biso min: 3.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å21.16 Å2
2---1.11 Å20 Å2
3---2.63 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 0 75 3306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223339
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9924547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5245412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11622.078154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65415565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3131541
X-RAY DIFFRACTIONr_chiral_restr0.1040.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0222567
X-RAY DIFFRACTIONr_mcbond_it0.7661.52066
X-RAY DIFFRACTIONr_mcangle_it1.29723355
X-RAY DIFFRACTIONr_scbond_it2.19231273
X-RAY DIFFRACTIONr_scangle_it3.2164.51189
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 136 -
Rwork0.284 2634 -
all-2770 -
obs--95.58 %
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)
13.25860.24490.39851.82640.29161.2880.1711-0.2315-0.010.2017-0.0698-0.2510.13280.0388-0.10130.0529-0.02080.01340.1335-0.03930.19569.852-0.46126.344
24.1327-0.93710.3661.55480.31271.54160.0583-0.0379-0.07080.03010.0479-0.09990.0508-0.1614-0.10630.0401-0.02670.04440.15460.00160.1001-15.3760.84214.9
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 205
2X-RAY DIFFRACTION1A216 - 246
3X-RAY DIFFRACTION2B1 - 206
4X-RAY DIFFRACTION2B216 - 259

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