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- PDB-1bg8: HDEA FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1bg8
TitleHDEA FROM ESCHERICHIA COLI
ComponentsHDEA
KeywordsPERIPLASMIC / HDEA
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 / MIR / Resolution: 2.2 Å
AuthorsYang, F. / Gustafson, K.R. / Boyd, M.R. / Wlodawer, A.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure of Escherichia coli HdeA.
Authors: Yang, F. / Gustafson, K.R. / Boyd, M.R. / Wlodawer, A.
History
DepositionJun 5, 1998Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HDEA
B: HDEA
C: HDEA


Theoretical massNumber of molelcules
Total (without water)29,2593
Polymers29,2593
Non-polymers00
Water4,089227
1
A: HDEA
B: HDEA


Theoretical massNumber of molelcules
Total (without water)19,5062
Polymers19,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-22 kcal/mol
Surface area7900 Å2
MethodPISA
2
C: HDEA

C: HDEA


Theoretical massNumber of molelcules
Total (without water)19,5062
Polymers19,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)47.476, 76.149, 73.607
Angle α, β, γ (deg.)90.00, 98.93, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.543515, -0.785768, 0.29523), (-0.784686, -0.600528, -0.153735), (0.298094, -0.148105, -0.942977)28.9373, 74.098, 45.8945
2given(0.387864, 0.887464, 0.248936), (0.884061, -0.434601, 0.171922), (0.260763, 0.153392, -0.953139)-43.8004, -9.4342, 12.5702

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Components

#1: Protein HDEA / 10K-S PROTEIN / HYPOTHETICAL PROTEIN A


Mass: 9752.882 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P26604, UniProt: P0AES9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growpH: 3.6
Details: 36% PEG400, 5% GLYCEROL, 50MM SODIUM CITRATE, PH 3.6
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
136 %PEG4001reservoir
25 %glycerol1reservoir
350 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 16, 1998 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 12863 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.071 / Net I/σ(I): 8.4
Reflection shellResolution: 2.2→2.26 Å / Rsym value: 0.473 / % possible all: 94.8
Reflection
*PLUS
Rmerge(I) obs: 0.071

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1096 10 %RANDOM
Rwork0.163 ---
obs0.163 11106 85 %-
Displacement parametersBiso mean: 40.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 0 227 1988
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.756
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.36
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.634
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight Biso Weight position
11RESTRAINTS WERE APPLIED TO MAIN CHAIN AND SIDE CHAIN ATOMS SEPARATELYX-RAY DIFFRACTION0.0592300
22X-RAY DIFFRACTION0.0612300
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.288 108 6.63 %
Rwork0.267 966 -
obs--65.9 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.365
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.634

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