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- PDB-4xvv: Crystal structure of an Acid stress chaperone HdeB (KPN_03484) fr... -

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Basic information

Entry
Database: PDB / ID: 4xvv
TitleCrystal structure of an Acid stress chaperone HdeB (KPN_03484) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.70 A resolution
ComponentsAcid stress chaperone HdeB
KeywordsCHAPERONE / HdeA family protein (PF06411) / protein HNS-dependent expression A fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


cellular stress response to acidic pH / unfolded protein binding / periplasmic space
Similarity search - Function
HNS-dependent expression B / 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 HdeB
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM094586 United States
CitationJournal: To be published
Title: Crystal structure of an Acid stress chaperone HdeB (KPN_03484) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 1, 2023Group: Data collection / Database references
Category: database_2 / diffrn_radiation_wavelength / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acid stress chaperone HdeB
B: Acid stress chaperone HdeB


Theoretical massNumber of molelcules
Total (without water)17,8072
Polymers17,8072
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-17 kcal/mol
Surface area7400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.475, 39.443, 98.256
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Acid stress chaperone HdeB


Mass: 8903.292 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
Gene: hdeB, KPN_03484 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6TE95
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 26-101 OF THE TARGET SEQUENCE.

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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: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M ammonium sulfate, 30.0% polyethylene glycol monomethyl ether 2000, 0.1M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979559 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2014 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979559 Å / Relative weight: 1
ReflectionResolution: 1.7→29.286 Å / Num. obs: 15930 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 3.62 % / Biso Wilson estimate: 29.463 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.069 / Net I/σ(I): 9.32 / Num. measured all: 61343
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
1.7-1.760.5730.7081.65554296427970.948194.4
1.76-1.830.7280.4812.46288302729290.64296.8
1.83-1.910.7930.3883.16062291428320.51697.2
1.91-2.020.8720.26156853327331900.34597.5
2.02-2.140.9420.17475980285827800.22897.3
2.14-2.310.9670.1199.26330306029430.15896.2
2.31-2.540.9850.08511.26118297828460.11395.6
2.54-2.90.9910.05913.96080296228060.07994.7
2.9-3.660.9960.03918.56052306128190.05292.1
3.660.9970.02922.16026303228140.03992.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SOLVEphasing
XSCALEJanuary 10, 2014 BUILT=20140307data scaling
REFMAC5.7.0032refinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→29.286 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 4.934 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.116
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 808 5.1 %RANDOM
Rwork0.1966 15080 --
obs0.198 15888 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 87.56 Å2 / Biso mean: 33.9187 Å2 / Biso min: 16.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 0 76 1254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191263
X-RAY DIFFRACTIONr_bond_other_d0.0040.021164
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9711726
X-RAY DIFFRACTIONr_angle_other_deg1.1243.0032704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7775163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.89726.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7315183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.547153
X-RAY DIFFRACTIONr_chiral_restr0.0850.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211450
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02273
X-RAY DIFFRACTIONr_mcbond_it1.7113.22619
X-RAY DIFFRACTIONr_mcbond_other1.73.209618
X-RAY DIFFRACTIONr_mcangle_it2.6815.992775
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 63 -
Rwork0.355 1028 -
all-1091 -
obs--93.25 %
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)
14.8594-1.4482-1.24662.91720.02112.40090.15190.21840.10480.0353-0.1992-0.005-0.3126-0.12070.04740.1661-0.007-0.01040.06390.01280.02890.7524.0325.517
22.66140.70851.05752.1447-0.16274.07240.02050.014-0.220.3556-0.0163-0.24330.3040.3377-0.00410.22130.0194-0.01690.08370.01950.07554.46210.43914.068
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 101
2X-RAY DIFFRACTION2B27 - 99

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