PDB-7mhb: Crystal structure of ATP-dependent protease ATPase subunit HslU i...

ID or keywords:

Entry

Database: PDB / ID: 7mhb

Title

Crystal structure of ATP-dependent protease ATPase subunit HslU in complex with Adenosine 5'-diphosphate

Components

ATP-dependent protease ATPase subunit HslU

Keywords

CHAPERONE / SSGCID / structural genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

HslUV protease complex / protein unfolding / peptidase activity / ATP binding
Similarity search - Function

Biological species

Brucella abortus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of ATP-dependent protease ATPase subunit HslU in complex with Adenosine 5'-diphosphate
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Apr 15, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 28, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7mhb.cif.gz	303.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7mhb.ent.gz	203.1 KB	Display	PDB format
PDBx/mmJSON format	7mhb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7mhb_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	7mhb_full_validation.pdf.gz	1.1 MB	Display
Data in XML	7mhb_validation.xml.gz	23.4 KB	Display
Data in CIF	7mhb_validation.cif.gz	32 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mh/7mhb ftp://data.pdbj.org/pub/pdb/validation_reports/mh/7mhb	HTTPS FTP

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Related structure data

Related structure data	1ofhS S: Starting model for refinement
Similar structure data	6ufq-d 6eer-d 6ubn-d 6byw-d 6ubz-d 6ubr-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: BrabA.00053.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (5) #176 - Aug 2014 Dynein similarity (5)

Deposited unit

A: ATP-dependent protease ATPase subunit HslU

B: ATP-dependent protease ATPase subunit HslU

hetero molecules

95.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ATP-dependent protease ATPase subunit HslU

B: ATP-dependent protease ATPase subunit HslU

hetero molecules

x 6

defined by author&software
Evidence: gel filtration
575 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-y,x-y,z	1
crystal symmetry operation	3_555	-x+y,-x,z	1
crystal symmetry operation	4_555	y,x,-z	1
crystal symmetry operation	5_555	x-y,-y,-z	1
crystal symmetry operation	6_555	-x,-x+y,-z	1

Unit cell

Length a, b, c (Å)	191.750, 191.750, 147.660
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	155
Space group name H-M	H32
Space group name Hall	R32"
Symmetry operation	#1: x,y,z #2: -y,x-y,z #3: -x+y,-x,z #4: x-y,-y,-z #5: -x,-x+y,-z #6: y,x,-z #7: x+1/3,y+2/3,z+2/3 #8: -y+1/3,x-y+2/3,z+2/3 #9: -x+y+1/3,-x+2/3,z+2/3 #10: x-y+1/3,-y+2/3,-z+2/3 #11: -x+1/3,-x+y+2/3,-z+2/3 #12: y+1/3,x+2/3,-z+2/3 #13: x+2/3,y+1/3,z+1/3 #14: -y+2/3,x-y+1/3,z+1/3 #15: -x+y+2/3,-x+1/3,z+1/3 #16: x-y+2/3,-y+1/3,-z+1/3 #17: -x+2/3,-x+y+1/3,-z+1/3 #18: y+2/3,x+1/3,-z+1/3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 3 through 40 or (resid 41...
d_2	ens_1	(chain "B" and (resid 3 through 6 or (resid 7...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	ASN	GLY	A	1 - 88
d_1	2	ens_1	VAL	GLU	A	90 - 115
d_1	3	ens_1	ASP	GLY	A	117 - 306
d_1	4	ens_1	ADP	ADP	B
d_1	5	ens_1	SO4	SO4	C
d_1	6	ens_1	SO4	SO4	D
d_1	7	ens_1	SO4	SO4	E
d_1	8	ens_1	EDO	EDO	F
d_1	9	ens_1	EDO	EDO	G
d_2	1	ens_1	ASN	GLY	H	1 - 88
d_2	2	ens_1	VAL	GLY	H	90 - 305
d_2	3	ens_1	ADP	ADP	I
d_2	4	ens_1	SO4	SO4	J
d_2	5	ens_1	SO4	SO4	K
d_2	6	ens_1	SO4	SO4	L
d_2	7	ens_1	EDO	EDO	M
d_2	8	ens_1	EDO	EDO	N

NCS oper: (Code: givenMatrix: (0.491963345414, -0.870615013619, 0.00125093186451), (-0.870574817643, -0.49195357639, -0.00900919321984), (0.00845893928235, 0.00334316305609, -0.999958633948)Vector: - ...

#1: Protein	ATP-dependent protease ATPase subunit HslU / Unfoldase HslU Mass: 47072.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus (bacteria) / Strain: 2308 / Gene: hslU, BAB1_2080 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2YQZ4
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.79 Å³/Da / Density % sol: 56 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Anatrace/Calibre MCSG1 screen, condition G3: 1.5M Ammonium sulfate, 100mM Bis-Tris Propane: HCl, pH 7: Braba.00053.a.AE5.PW38673 at 20mg/ml: tray 311683 G3: cryo: 25% EG: puck akp6-1.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 3, 2020 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.6→50 Å / Num. obs: 32080 / % possible obs: 99.9 % / Redundancy: 9.33 % / B_iso Wilson estimate: 61.138 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.088 / R_rim(I) all: 0.093 / Χ²: 0.914 / Net I/σ(I): 16.03

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.6-2.67	9.496	0.595	4.11	2352	0.94	0.628	100
2.67-2.74	9.479	0.468	4.92	2305	0.97	0.495	100
2.74-2.82	9.487	0.455	5.25	2231	0.967	0.481	100
2.82-2.91	9.476	0.349	6.63	2159	0.978	0.369	100
2.91-3	9.447	0.278	8.11	2101	0.986	0.294	100
3-3.11	9.392	0.228	9.73	2043	0.989	0.241	100
3.11-3.22	9.401	0.179	11.87	1960	0.993	0.19	99.9
3.22-3.36	9.318	0.146	14.41	1907	0.993	0.155	100
3.36-3.51	9.294	0.122	16.72	1796	0.996	0.129	100
3.51-3.68	9.24	0.1	19.75	1745	0.996	0.106	99.9
3.68-3.88	9.25	0.093	20.86	1650	0.997	0.098	99.9
3.88-4.11	9.21	0.079	24.36	1575	0.997	0.084	100
4.11-4.39	9.203	0.07	26.58	1470	0.996	0.075	100
4.39-4.75	9.245	0.066	29.02	1381	0.997	0.07	100
4.75-5.2	9.253	0.065	28.74	1269	0.997	0.069	100
5.2-5.81	9.294	0.063	29.05	1163	0.997	0.067	100
5.81-6.71	9.25	0.06	29.51	1035	0.997	0.064	100
6.71-8.22	9.178	0.053	31.54	871	0.998	0.056	100
8.22-11.63	9.049	0.045	33.14	673	0.999	0.048	100
11.63-50	8.102	0.042	31.69	394	0.998	0.045	96.8

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19 dev 4203	refinement
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 1ofh in two domains as per Morda

1ofh

Resolution: 2.6→39.97 Å / SU ML: 0.3723 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.6314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2878	1993	6.22 %	0
R_work	0.2482	30065	-	-
obs	0.2507	32058	99.91 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 67.97 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→39.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4563	0	100	73	4736

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0046	4731
X-RAY DIFFRACTION	f_angle_d	0.7488	6430
X-RAY DIFFRACTION	f_chiral_restr	0.0473	779
X-RAY DIFFRACTION	f_plane_restr	0.0054	848
X-RAY DIFFRACTION	f_dihedral_angle_d	14.3848	1732

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.779377779196 Å

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6-2.66	0.353	142	0.3128	2122	X-RAY DIFFRACTION	99.96
2.67-2.74	0.3412	144	0.3091	2128	X-RAY DIFFRACTION	99.78
2.74-2.82	0.4164	147	0.3055	2121	X-RAY DIFFRACTION	99.87
2.82-2.91	0.3136	152	0.2776	2126	X-RAY DIFFRACTION	99.96
2.91-3.01	0.3588	134	0.2929	2127	X-RAY DIFFRACTION	99.96
3.01-3.13	0.3511	130	0.3075	2151	X-RAY DIFFRACTION	99.96
3.13-3.28	0.3316	140	0.292	2140	X-RAY DIFFRACTION	99.82
3.28-3.45	0.3087	121	0.2684	2166	X-RAY DIFFRACTION	100
3.45-3.66	0.2721	150	0.2524	2130	X-RAY DIFFRACTION	99.96
3.66-3.95	0.3008	139	0.2434	2134	X-RAY DIFFRACTION	99.87
3.95-4.34	0.2753	146	0.2144	2166	X-RAY DIFFRACTION	100
4.34-4.97	0.2293	136	0.2042	2155	X-RAY DIFFRACTION	100
4.97-6.26	0.2762	147	0.2457	2175	X-RAY DIFFRACTION	100
6.26-39.97	0.2649	165	0.2303	2224	X-RAY DIFFRACTION	99.67

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.17917874522	0.735918270704	0.29894447156	1.67423879334	0.630306650339	0.566480012946	-0.0594112434691	-0.370134068938	0.173778859376	0.480504885513	-0.199068971799	0.419935925795	0.00339917421877	-0.355128360095	0.205125679249	0.44483683685	0.0597816997838	0.0930995738064	0.611878738127	-0.171507515278	0.515669512621	-32.6856458445	10.6861425251	23.3295301767
2	0.459441216122	1.17911322303	1.26305586175	3.51290141656	4.14236152836	5.14629269703	-0.523139016325	-1.25223798207	0.137954774187	1.34612753193	0.257326286949	-0.299310815571	0.235139821797	0.915841329583	0.388011830971	0.899301161746	0.13847626235	-0.0133607704787	1.00305957182	-0.101828722735	0.428012451885	-23.0716182665	8.37934913617	36.189315681
3	6.28865330097	-2.99819484488	0.0143763337535	4.92981763325	-1.98628425285	2.97703561134	-0.324304413864	-0.410847172297	-0.153560330179	0.176332958002	-0.0329348190941	-0.0207090755626	-0.0370005180526	0.0633127492222	0.312172477207	0.389945539245	-0.0254912371488	0.0129283219198	0.467755093738	-0.103339602549	0.377464030155	-22.4082354498	2.38492812227	18.8089418403
4	1.73576029692	0.440667496925	-0.0512164695834	3.52674890306	0.0742483892668	0.519305816649	0.0946450646255	-0.101495358823	0.585926702748	-0.00718316522964	-0.268403353437	0.281923793122	-0.274354602833	-0.227797609697	0.124943548214	0.528426257041	0.0906113761999	-0.00597432244311	0.557138062286	-0.166427760477	0.628561482515	-28.4210270117	31.6973963622	14.335484415
5	0.580957076372	-0.708044677023	-0.496851377836	1.75813042047	0.989822902448	0.588171942485	-0.112074779173	0.709880487182	0.209533338094	-0.402525122417	-0.416293839513	0.317293519031	-0.552153472192	-0.428134756521	0.432214407479	0.666901995112	0.154361506672	-0.271658072476	0.808829036539	-0.100189408895	0.853965743255	-38.4360913172	25.333909052	-24.5908164968
6	1.24586269627	0.749993335544	0.072804949327	1.30013671001	0.560703949037	0.665069724741	-0.120123411363	0.583620219924	0.263994364184	-0.368190399037	-0.0241916681067	0.299313325122	-0.254028787217	-0.0931116129214	0.0766061604864	0.500454051378	0.0664990417063	-0.191660757771	0.57457505497	0.00876611639842	0.44150437402	-22.629409013	22.106422883	-22.841185238
7	1.36554179512	-0.390416093729	0.511672304058	0.357669312044	-0.172942298457	0.191827758186	0.39566012378	2.13561103615	-0.183816446081	-0.683626927573	-0.481053642338	0.260375169867	0.89047592709	0.271902593187	-0.0220085763413	0.698738402263	0.115993480976	-0.146246399811	1.37134013912	-0.0158210038086	0.308024469157	-18.7766074888	15.2027956185	-35.8131050993
8	9.59545600472	-2.05933401865	-1.35525293301	4.95800311585	-0.000947230407248	2.21022779754	-0.253264560149	-0.204575015358	0.13712437855	0.0972369957615	0.150614021434	-0.0903675746978	0.102702301376	-0.0708192175162	0.079251795326	0.344331446555	-0.01655229275	-0.0481064657604	0.330651432254	-0.0548330466426	0.301527067907	-13.1548805905	16.5822346302	-13.1463977636
9	3.38475208536	0.579440366427	0.185387376939	2.03873638676	-0.113203721705	0.623393089417	-0.00725744195223	0.169475340574	0.112791103915	-0.151669816493	-0.199517715409	0.539159208687	0.0232034912912	-0.223727788467	0.173387199578	0.446713498323	0.0610862147354	-0.13283402437	0.532936170426	-0.0872119354435	0.469520206111	-34.4514415096	13.4504760748	-15.8802243701
10	0.250893278452	-0.255543886557	-0.595404757787	8.07198576479	3.14201036053	2.23347821984	0.125705590548	0.804948263362	-0.811494159628	-0.0730789863398	0.205709617868	1.35124026046	0.325742299285	-0.060058985201	0.0875961101962	0.470553270641	0.0139096348158	-0.230225354228	0.749069374439	-0.271170661577	0.912531718446	-54.3535547806	-4.56362999642	-18.8604842997

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 3 through 95 )	A	A	3 - 95	1 - 93
2	2	chain 'A' and (resid 96 through 241 )	A	A	96 - 241	94 - 130
3	3	chain 'A' and (resid 242 through 299 )	A	A	242 - 299	131 - 186
4	4	chain 'A' and (resid 300 through 419 )	A	A	300 - 419	187 - 306
5	5	chain 'B' and (resid 3 through 20 )	B	H	3 - 20	1 - 18
6	6	chain 'B' and (resid 21 through 95 )	B	H	21 - 95	19 - 93
7	7	chain 'B' and (resid 96 through 241 )	B	H	96 - 241	94 - 129
8	8	chain 'B' and (resid 242 through 277 )	B	H	242 - 277	130 - 163
9	9	chain 'B' and (resid 278 through 393 )	B	H	278 - 393	164 - 279
10	10	chain 'B' and (resid 394 through 419 )	B	H	394 - 419	280 - 305

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