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- PDB-1vpz: Crystal structure of a putative carbon storage regulator protein ... -

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Basic information

Entry
Database: PDB / ID: 1vpz
TitleCrystal structure of a putative carbon storage regulator protein (csra, pa0905) from pseudomonas aeruginosa at 2.05 A resolution
ComponentsCarbon storage regulator homolog
KeywordsRNA BINDING PROTEIN / Csra-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


regulation of secondary metabolic process / regulation of single-species biofilm formation / protein secretion by the type VI secretion system / regulation of carbohydrate metabolic process / quorum sensing / protein secretion by the type III secretion system / mRNA catabolic process / positive regulation of translational initiation / negative regulation of translational initiation / mRNA 5'-UTR binding / cytosol
Similarity search - Function
Translational regulator CsrA / Carbon storage regulator superfamily / Global regulator protein family
Similarity search - Domain/homology
Translational regulator CsrA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 A resolution reveals a new fold.
Authors: Rife, C. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Ambing, E. / Axelrod, H. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Godzik, A. / ...Authors: Rife, C. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Ambing, E. / Axelrod, H. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Han, G.W. / Haugen, J. / Hornsby, M. / Jaroszewski, L. / Klock, H.E. / Koesema, E. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Miller, M.D. / Moy, K. / Nigoghossian, E. / Paulsen, J. / Quijano, K. / Reyes, R. / Sims, E. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / White, A. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionNov 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbon storage regulator homolog
B: Carbon storage regulator homolog


Theoretical massNumber of molelcules
Total (without water)17,0452
Polymers17,0452
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-25 kcal/mol
Surface area6850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.066, 56.669, 98.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 1 - 53 / Label seq-ID: 13 - 65

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

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Components

#1: Protein Carbon storage regulator homolog


Mass: 8522.276 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: csrA / Production host: Escherichia coli (E. coli) / References: UniProt: O69078
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 3.7
Details: 30.0% MPD, 0.1M Phosphate Citrate pH 3.7, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 5.0.210.979508
SYNCHROTRONALS 5.0.220.979508,0.961114
DetectorType: ADSC / Detector: CCD / Date: Nov 10, 2004 / Details: fixed-height exit beam, toroidal focusing mirror
RadiationMonochromator: Double-crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9795081
20.9611141
ReflectionResolution: 2.05→27.23 Å / Num. obs: 8735 / % possible obs: 97.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 47.8 Å2 / Rsym value: 0.075 / Net I/σ(I): 11.4
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 562 / Rsym value: 0.365 / % possible all: 85.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.05→24.59 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 13.773 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.191
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: NO DENSITY FOR RESIDUES A56-62, B54-62. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27545 422 4.8 %RANDOM
Rwork0.21848 ---
obs0.22092 8281 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.776 Å2
Baniso -1Baniso -2Baniso -3
1-4.76 Å20 Å20 Å2
2---1.02 Å20 Å2
3----3.74 Å2
Refinement stepCycle: LAST / Resolution: 2.05→24.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 0 0 23 891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022887
X-RAY DIFFRACTIONr_bond_other_d0.0020.02876
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9431198
X-RAY DIFFRACTIONr_angle_other_deg0.77532002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2275111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22522.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80315164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4521511
X-RAY DIFFRACTIONr_chiral_restr0.090.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02970
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02173
X-RAY DIFFRACTIONr_nbd_refined0.1920.2126
X-RAY DIFFRACTIONr_nbd_other0.1990.2837
X-RAY DIFFRACTIONr_nbtor_other0.090.2593
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.22
X-RAY DIFFRACTIONr_mcbond_it2.233569
X-RAY DIFFRACTIONr_mcbond_other0.6153238
X-RAY DIFFRACTIONr_mcangle_it3.0855907
X-RAY DIFFRACTIONr_scbond_it5.5158336
X-RAY DIFFRACTIONr_scangle_it8.06111291
X-RAY DIFFRACTIONr_nbtor_refined0.170.2397
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 767 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.630.5
medium thermal0.992
LS refinement shellResolution: 2.051→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 37 6.65 %
Rwork0.302 519 -
obs--84.89 %
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)
13.194-0.95370.55962.0674-0.24035.3954-0.0972-0.08450.04260.22170.1-0.10590.0139-0.1244-0.0028-0.17930.00580.0026-0.0818-0.0117-0.14251.37528.20736.493
22.3546-0.2458-0.34283.1313-0.56454.973-0.05550.00520.0399-0.0940.0644-0.1521-0.0459-0.0921-0.0089-0.25540.00590.0103-0.0472-0.0173-0.1302-0.89232.71137.308
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-1 - 5411 - 66
22BB-2 - 5310 - 65

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