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- PDB-1dj8: CRYSTAL STRUCTURE OF E. COLI PERIPLASMIC PROTEIN HDEA -

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Basic information

Entry
Database: PDB / ID: 1dj8
TitleCRYSTAL STRUCTURE OF E. COLI PERIPLASMIC PROTEIN HDEA
ComponentsPROTEIN HNS-DEPENDENT EXPRESSION A
KeywordsSTRUCTURAL PROTEIN / ALPHA HELICAL
Function / homology
Function and homology information


cellular stress response to acidic pH / cellular response to acidic pH / : / protein folding chaperone / unfolded protein binding / protein-folding chaperone binding / outer membrane-bounded periplasmic space / protein homodimerization activity / identical protein binding
Similarity search - Function
HNS-dependent expression A / HNS-dependent expression A superfamily / HNS-dependent expression A / HNS-dependent expression A/B / HNS-dependent expression A/B superfamily / HdeA/HdeB family / 10k-s Protein, Hypothetical Protein A; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Acid stress chaperone HdeA / Acid stress chaperone HdeA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsGajiwala, K.S. / Burley, S.K.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: HDEA, a periplasmic protein that supports acid resistance in pathogenic enteric bacteria.
Authors: Gajiwala, K.S. / Burley, S.K.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal Structure of Escherichia coli HdeA
Authors: Yang, F. / Gustafson, K.R. / Boyd, M.R. / Wlodawer, A.
#2: Journal: Electrophoresis / Year: 1997
Title: Comparing the Predicted and Observed Properties of Proteins Encoded in the Genome of Escherichia coli K-12
Authors: Link, A.J. / Robinson, K. / Church, G.H.
#3: Journal: Mol.Microbiol. / Year: 1996
Title: Identification of Sigma S-Dependent Genes Associated with the Stationary-Phase Acid-Resistance Phenotype of Shigella flexneri
Authors: Waterman, S.R. / Small, P.L.
#4: Journal: Biochem.Biophys.Res.Commun. / Year: 1996
Title: Evidence for GroES Acting as Transcriptional Regulator
Authors: Legname, G. / Buono, P. / Fossati, G. / Monzini, N. / Mascagni, P. / Modena, D. / Marcucci, F.
#5: Journal: Mol.Microbiol. / Year: 1997
Title: H-NS: a Modulator of Environmentally Regulated Gene Expression
Authors: Atlung, T. / Ingmer, H.
History
DepositionDec 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 99Author sent a new reflection file to supercede the initially released SF file in December, 1999.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN HNS-DEPENDENT EXPRESSION A
B: PROTEIN HNS-DEPENDENT EXPRESSION A
C: PROTEIN HNS-DEPENDENT EXPRESSION A
D: PROTEIN HNS-DEPENDENT EXPRESSION A
E: PROTEIN HNS-DEPENDENT EXPRESSION A
F: PROTEIN HNS-DEPENDENT EXPRESSION A


Theoretical massNumber of molelcules
Total (without water)58,5176
Polymers58,5176
Non-polymers00
Water7,008389
1
A: PROTEIN HNS-DEPENDENT EXPRESSION A
B: PROTEIN HNS-DEPENDENT EXPRESSION A


Theoretical massNumber of molelcules
Total (without water)19,5062
Polymers19,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-24 kcal/mol
Surface area8510 Å2
MethodPISA
2
C: PROTEIN HNS-DEPENDENT EXPRESSION A
D: PROTEIN HNS-DEPENDENT EXPRESSION A


Theoretical massNumber of molelcules
Total (without water)19,5062
Polymers19,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-24 kcal/mol
Surface area8680 Å2
MethodPISA
3
E: PROTEIN HNS-DEPENDENT EXPRESSION A
F: PROTEIN HNS-DEPENDENT EXPRESSION A


Theoretical massNumber of molelcules
Total (without water)19,5062
Polymers19,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-25 kcal/mol
Surface area8880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.0, 73.6, 74.3
Angle α, β, γ (deg.)90.0, 96.8, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROTEIN HNS-DEPENDENT EXPRESSION A / HDEA


Mass: 9752.882 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cellular location: PERIPLASM / References: UniProt: P26604, UniProt: P0AES9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4
Details: PEG1500, SODIUM ACETATE, pH 4, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
25 mmsodium acetate1drop
3100 mMsodium acetate1reservoir
426-30 %(w/v)PEG15001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: OTHER / Detector: CCD / Date: Dec 5, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 33169 / Num. obs: 32222 / % possible obs: 97.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 12 / Redundancy: 8 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.123 / % possible all: 97.7
Reflection shell
*PLUS
% possible obs: 97.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2→15 Å / σ(F): 3 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3238 -RANDOM
Rwork0.209 ---
all0.209 34032 --
obs0.209 32453 95.4 %-
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3678 0 0 389 4067
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.73
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: 'CNS' / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rwork: 0.246

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