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- PDB-1g3k: CRYSTAL STRUCTURE OF THE H. INFLUENZAE PROTEASE HSLV AT 1.9 A RES... -

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Basic information

Entry
Database: PDB / ID: 1g3k
TitleCRYSTAL STRUCTURE OF THE H. INFLUENZAE PROTEASE HSLV AT 1.9 A RESOLUTION
ComponentsATP-DEPENDENT PROTEASE HSLV
KeywordsHYDROLASE
Function / homology
Function and homology information


HslU-HslV peptidase / HslUV protease complex / proteasome core complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / metal ion binding / cytoplasm
Similarity search - Function
ATP-dependent protease, HslV subunit / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent protease subunit HslV
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSousa, M.C. / McKay, D.B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Crystal and solution structures of an HslUV protease-chaperone complex.
Authors: Sousa, M.C. / Trame, C.B. / Tsuruta, H. / Wilbanks, S.M. / Reddy, V.S. / McKay, D.B.
History
DepositionOct 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 600HETEROGEN HOH 201-270 IS ASSOCIATED WITH CHAIN A. HOH 1201-1269 IS ASSOCIATED WITH CHAIN B. HOH ...HETEROGEN HOH 201-270 IS ASSOCIATED WITH CHAIN A. HOH 1201-1269 IS ASSOCIATED WITH CHAIN B. HOH 2201-2260 IS ASSOCIATED WITH CHAIN C.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-DEPENDENT PROTEASE HSLV
B: ATP-DEPENDENT PROTEASE HSLV
C: ATP-DEPENDENT PROTEASE HSLV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7806
Polymers56,7113
Non-polymers693
Water3,567198
1
A: ATP-DEPENDENT PROTEASE HSLV
B: ATP-DEPENDENT PROTEASE HSLV
C: ATP-DEPENDENT PROTEASE HSLV
hetero molecules

A: ATP-DEPENDENT PROTEASE HSLV
B: ATP-DEPENDENT PROTEASE HSLV
C: ATP-DEPENDENT PROTEASE HSLV
hetero molecules

A: ATP-DEPENDENT PROTEASE HSLV
B: ATP-DEPENDENT PROTEASE HSLV
C: ATP-DEPENDENT PROTEASE HSLV
hetero molecules

A: ATP-DEPENDENT PROTEASE HSLV
B: ATP-DEPENDENT PROTEASE HSLV
C: ATP-DEPENDENT PROTEASE HSLV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,11824
Polymers226,84312
Non-polymers27612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area29490 Å2
ΔGint-257 kcal/mol
Surface area71480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.018, 121.799, 126.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a dodecamer which can be constructed as follows: 1) Take chains A,B and C, apply symm op x,-y,-z, and translate 0 0 1 2) Finally take all six chains and apply symm op -x,-y,z

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Components

#1: Protein ATP-DEPENDENT PROTEASE HSLV


Mass: 18903.549 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P43772, EC: 3.4.99.-
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Sodium Citrate, PEG 400, HCl Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Details: This particular structure is not described in this paper.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-20 mg/mlprotein1drop
210 mMMOPS1drop
31 mM1dropMg(OAc)2
41 mMATP1drop
53-6 %PEG2000MME1reservoir
61 M1reservoirKCl
710 mM1reservoirMg(OAc)2
850 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 48317 / Num. obs: 48317 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 28.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 7.3 / Num. unique all: 4815 / % possible all: 100
Reflection
*PLUS

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: E. Coli HslV at 3.8A

Resolution: 1.9→29.34 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3798393.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 4870 10.1 %RANDOM
Rwork0.2 ---
obs0.201 48233 99.9 %-
all-48281 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.17 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.84 Å20 Å20 Å2
2---3.77 Å20 Å2
3----2.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3837 0 3 198 4038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 847 10.6 %
Rwork0.219 7120 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
LS refinement shell
*PLUS
Rfactor Rfree: 0.258 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.219

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