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- PDB-1sf8: Crystal structure of the carboxy-terminal domain of htpG, the E. ... -

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Basic information

Entry
Database: PDB / ID: 1sf8
TitleCrystal structure of the carboxy-terminal domain of htpG, the E. coli Hsp90
ComponentsChaperone protein htpG
KeywordsCHAPERONE / four helix bundle dimerization interface / exposed amphipathic helix / three stranded beta sheet
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / protein folding chaperone / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / protein-folding chaperone binding / response to heat / DNA damage response / protein homodimerization activity / ATP hydrolysis activity ...FtsZ-dependent cytokinesis / protein folding chaperone / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / protein-folding chaperone binding / response to heat / DNA damage response / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Heat shock protein 90, C-terminal domain / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-like ATPases ...Heat shock protein 90, C-terminal domain / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Chaperone protein HtpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsHarris, S.F. / Shiau, A.K. / Agard, D.A.
CitationJournal: Structure / Year: 2004
Title: The crystal structure of the carboxy-terminal dimerization domain of htpG, the Escherichia coli Hsp90, reveals a potential substrate binding site.
Authors: Harris, S.F. / Shiau, A.K. / Agard, D.A.
History
DepositionFeb 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperone protein htpG
B: Chaperone protein htpG
C: Chaperone protein htpG
D: Chaperone protein htpG
E: Chaperone protein htpG
F: Chaperone protein htpG
G: Chaperone protein htpG
H: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,29114
Polymers116,0088
Non-polymers2826
Water8,719484
1
A: Chaperone protein htpG
G: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0613
Polymers29,0022
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-18 kcal/mol
Surface area13520 Å2
MethodPISA
2
C: Chaperone protein htpG
E: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0964
Polymers29,0022
Non-polymers942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-35 kcal/mol
Surface area13170 Å2
MethodPISA
3
D: Chaperone protein htpG
F: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0964
Polymers29,0022
Non-polymers942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-31 kcal/mol
Surface area12860 Å2
MethodPISA
4
B: Chaperone protein htpG
H: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0383
Polymers29,0022
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-26 kcal/mol
Surface area12750 Å2
MethodPISA
5
A: Chaperone protein htpG
G: Chaperone protein htpG
hetero molecules

B: Chaperone protein htpG
H: Chaperone protein htpG
hetero molecules

C: Chaperone protein htpG
D: Chaperone protein htpG
E: Chaperone protein htpG
F: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,29114
Polymers116,0088
Non-polymers2826
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation6_555x+1/2,-y+1/2,-z+1/41
crystal symmetry operation7_655y+1,x,-z1
identity operation1_555x,y,z1
Buried area12930 Å2
ΔGint-140 kcal/mol
Surface area47340 Å2
MethodPISA
6
C: Chaperone protein htpG
D: Chaperone protein htpG
E: Chaperone protein htpG
F: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1938
Polymers58,0044
Non-polymers1884
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-74 kcal/mol
Surface area24190 Å2
MethodPISA
7
A: Chaperone protein htpG
G: Chaperone protein htpG
hetero molecules

B: Chaperone protein htpG
H: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0986
Polymers58,0044
Non-polymers942
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z+1/41
Buried area5640 Å2
ΔGint-54 kcal/mol
Surface area24500 Å2
MethodPISA
8
F: Chaperone protein htpG
H: Chaperone protein htpG
hetero molecules

E: Chaperone protein htpG
G: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1698
Polymers58,0044
Non-polymers1654
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-y+1/2,x-1/2,z-1/41
Buried area4580 Å2
ΔGint-59 kcal/mol
Surface area25670 Å2
MethodPISA
9
A: Chaperone protein htpG
B: Chaperone protein htpG
C: Chaperone protein htpG
D: Chaperone protein htpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1226
Polymers58,0044
Non-polymers1172
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-44 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.516, 103.516, 249.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Chaperone protein htpG / Heat shock protein htpG / High temperature protein G / Heat shock protein C62.5


Mass: 14501.061 Da / Num. of mol.: 8 / Fragment: htpG residues 511 to 624 (natural C terminus)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HTPG, B0473, C0593, Z0590, ECS0526 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Z3
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 3.22 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium malonate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1271, 0.9791, 0.9790
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 23, 2002
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.12711
20.97911
30.9791
ReflectionResolution: 2.6→95.63 Å / Num. all: 79708 / Num. obs: 79708 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 39.1 Å2 / Limit h max: 39 / Limit h min: 0 / Limit k max: 28 / Limit k min: 0 / Limit l max: 95 / Limit l min: -96 / Observed criterion F max: 4416939.45 / Observed criterion F min: 10.74 / Rsym value: 0.063
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 2772 / Rsym value: 0.62 / % possible all: 70.5

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
MOSFLMdata reduction
ELVESdata reduction
SCALEPACKdata scaling
CCP4(SCALA)data scaling
ELVESdata scaling
MLPHAREphasing
ELVESphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→29.9 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3577 5 %random
Rwork0.223 ---
all0.225 ---
obs0.225 71994 90.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 46.1995 Å2 / ksol: 0.34476 e/Å3
Displacement parametersBiso max: 143.03 Å2 / Biso mean: 60.73 Å2 / Biso min: 18.06 Å2
Baniso -1Baniso -2Baniso -3
1-3.55 Å20 Å20 Å2
2--3.55 Å20 Å2
3----7.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.5 Å
Luzzati d res high-2.6
Refinement stepCycle: LAST / Resolution: 2.6→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7425 0 6 484 7915
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_torsion_deg21.1
X-RAY DIFFRACTIONc_torsion_impr_deg0.81
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.6-2.720.3629650.3555890.0219966588559.1
2.72-2.860.3933644.50.34877260.0219992809081
2.86-3.040.3584324.70.29787110.01710009914391.3
3.04-3.280.3174995.20.27190280.0149927952796
3.28-3.610.27848650.22692160.0139959970297.4
3.61-4.130.2634434.50.20594320.0129994987598.8
4.13-5.20.2245405.40.17793700.019985991099.2
5.2-95.630.215175.20.19293450.0099962986299
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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