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- PDB-1jjw: Structure of Haemophilus influenzae HslV Protein at 1.9 A Resolution -

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Basic information

Entry
Database: PDB / ID: 1jjw
TitleStructure of Haemophilus influenzae HslV Protein at 1.9 A Resolution
ComponentsATP-DEPENDENT PROTEASE HSLV
KeywordsHYDROLASE / K anomalous scattering / quasi-equivalent packing
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: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of Haemophilus influenzae HslV protein at 1.9 A resolution, revealing a cation-binding site near the catalytic site.
Authors: Sousa, M.C. / McKay, D.B.
History
DepositionJul 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_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: ATP-DEPENDENT PROTEASE HSLV
B: ATP-DEPENDENT PROTEASE HSLV
C: ATP-DEPENDENT PROTEASE HSLV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8286
Polymers56,7113
Non-polymers1173
Water3,441191
1
C: ATP-DEPENDENT PROTEASE HSLV
hetero molecules

C: ATP-DEPENDENT PROTEASE HSLV
hetero molecules

C: ATP-DEPENDENT PROTEASE HSLV
hetero molecules

C: ATP-DEPENDENT PROTEASE HSLV
hetero molecules

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

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

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

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


Theoretical massNumber of molelcules
Total (without water)227,31224
Polymers226,84312
Non-polymers46912
Water21612
TypeNameSymmetry operationNumber
crystal symmetry operation5_445x-1/2,y-1/2,z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation7_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation8_455x-1/2,-y+1/2,-z+1/21
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 area31080 Å2
ΔGint-128 kcal/mol
Surface area71820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.893, 122.331, 126.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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) / Gene: HslV / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P43772, EC: 3.4.99.-
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: sodium citrate, HCl Tris, PEG 400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein1drop
25 mM1dropMgCl2
31 mMADP1drop
410 mMMOPS1droppH7.0
530 %PEG4001reservoir
6100 mMsodium citrate1reservoir
7100 mMTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.55 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 6, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 46472 / Num. obs: 46472 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 28.8
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 9.1 / Rsym value: 0.195 / % possible all: 98.3

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G3K

1g3k


Resolution: 1.9→19.9 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3273928.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 8730 9.8 %RANDOM
Rwork0.215 ---
obs-88796 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.2708 Å2 / ksol: 0.36033 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å20 Å20 Å2
2---1.53 Å20 Å2
3----1.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 0 3 191 4040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 1435 9.8 %
Rwork0.254 13221 -
obs--94 %
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
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 9.8 % / Rfactor obs: 0.217 / Rfactor Rfree: 0.251
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Lowest resolution: 1.97 Å / Rfactor Rfree: 0.334 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.254 / Rfactor obs: 0.258

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