PDB-6u3l: Crystal structure of Hemerythrin HHE cation binding domain-contai...

ID or keywords:

Entry

Database: PDB / ID: 6u3l

Title

Crystal structure of Hemerythrin HHE cation binding domain-containing protein: Rv2633c homolog from Mycobacterium kansasii

Components

Hemerythrin HHE cation binding domain protein

Keywords

PROTEIN BINDING /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Hemerythrin-like / Hemerythrin HHE cation binding domain / Hemerythrin HHE cation binding domain protein / Hemerythrin HHE cation binding domain protein

Function and homology information

Biological species

Mycobacterium kansasii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.75 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Biochem.J. / Year: 2020
Title: Crystal structure of a hemerythrin-like protein from Mycobacterium kansasii and homology model of the orthologous Rv2633c protein of M. tuberculosis.
Authors: Ma, Z. / Abendroth, J. / Buchko, G.W. / Rohde, K.H. / Davidson, V.L.

History

Deposition	Aug 22, 2019	Deposition site: RCSB / Processing site: RCSB
Supersession	Jan 22, 2020	ID: 6PIE
Revision 1.0	Jan 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	Feb 12, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6u3l.cif.gz	98.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6u3l.ent.gz	62.4 KB	Display	PDB format
PDBx/mmJSON format	6u3l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u3/6u3l ftp://data.pdbj.org/pub/pdb/validation_reports/u3/6u3l	HTTPS FTP

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Related structure data

Related structure data	6q09C C: citing same article (ref.)
Similar structure data	4fr9-d 6q09-d 6tyj-d 6ltz-d 3ebq-d 6iuh-1 6pbi-2 3irb-1 1c6h-d 6pml-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-MykaA.20209.a TargetTrack: MykaA.20209.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hemerythrin HHE cation binding domain protein

hetero molecules

19.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	52.050, 52.050, 104.700
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21
Space group name Hall	P3₁2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3 #4: x-y,-y,-z+2/3 #5: -x,-x+y,-z+1/3 #6: y,x,-z

#1: Protein	Hemerythrin HHE cation binding domain protein Mass: 19533.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium kansasii (bacteria) / Gene: BZL29_7639 / Plasmid: MykaA.20209.a.B11 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) / References: UniProt: A0A1V3WIE5, UniProt: X7XZL2*PLUS
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 41.45 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: MCSG-1 screen F3: 200mM ammonium citrate, 25% PEG 3350: MykaA.20209.a.B11.PB00101 at 2mg/ml, grown at 14C: cryo: 20% EG: tray 308332F3: puck vlf8-4. For experimental phasing, a crystal from ...Details: MCSG-1 screen F3: 200mM ammonium citrate, 25% PEG 3350: MykaA.20209.a.B11.PB00101 at 2mg/ml, grown at 14C: cryo: 20% EG: tray 308332F3: puck vlf8-4. For experimental phasing, a crystal from MCSG-1 screen, condition F3 (200mM ammonium citrate, 25% PEG 3350) with MykaA.20209.a B1.PB00101 at 3mg/ml, grown at 14C, was incubated for 15 sec each in a solution of 90% reservoir and 10% 2.5M sodium iodide in ethylene glycol, and then in a solution of 80% reservoir and 20% 2.5M sodium iodide in ethylene glycol, and vitrified in liquid nitrogen: tray 308326f3: puck fdn8-5

Crystal

Density Matthews: 2.1 Å³/Da / Density % sol: 41.45 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop
Details: MCSG-1 screen F3: 200mM ammonium citrate, 25% PEG 3350: MykaA.20209.a.B11.PB00101 at 2mg/ml, grown at 14C: cryo: 20% EG: tray 308332F3: puck vlf8-4. For experimental phasing, a crystal from ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-F		1	0.97872
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.5418

Detector

Type	ID	Detector	Date
RAYONIX MX-300	1	CCD	Mar 21, 2010
RIGAKU SATURN 944+	2	CCD	Mar 18, 2010

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID	Monochromator
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2	C(111)

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97872	1
2	1.5418	1

Reflection

Resolution: 1.75→50 Å / Num. obs: 17189 / % possible obs: 100 % / Redundancy: 6.91 % / B_iso Wilson estimate: 28.21 Å² / CC_1/2: 1 / R_merge(I) obs: 0.041 / R_rim(I) all: 0.044 / Χ²: 1.052 / Net I/σ(I): 24.94

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
1.75-1.8	4.944	0.639	2.18	1264	0.85	0.716	99.9
1.8-1.84	6.278	0.552	3.11	1200	0.911	0.603	100
1.84-1.9	7.179	0.46	4.28	1177	0.944	0.496	100
1.9-1.96	7.279	0.344	5.69	1149	0.974	0.37	100
1.96-2.02	7.297	0.232	8.23	1123	0.987	0.249	100
2.02-2.09	7.21	0.174	10.88	1084	0.991	0.188	100
2.09-2.17	7.223	0.118	15.16	1044	0.996	0.128	100
2.17-2.26	7.222	0.096	18.98	1012	0.997	0.103	100
2.26-2.36	7.245	0.076	22.86	957	0.998	0.082	100
2.36-2.48	7.223	0.062	27.36	937	0.998	0.067	100
2.48-2.61	7.181	0.054	31.58	894	0.998	0.058	100
2.61-2.77	7.201	0.047	35.44	829	0.999	0.05	99.9
2.77-2.96	7.174	0.039	41.78	782	0.999	0.042	100
2.96-3.2	7.15	0.033	47.36	752	0.999	0.035	100
3.2-3.5	7.02	0.029	55.03	689	0.999	0.031	100
3.5-3.91	6.998	0.025	60.74	641	1	0.027	100
3.91-4.52	6.911	0.02	64.53	551	1	0.022	99.8
4.52-5.53	6.858	0.021	63.14	487	1	0.023	100
5.53-7.83	6.475	0.023	60.94	383	0.999	0.025	100
7.83-50	5.615	0.02	62.2	234	0.999	0.022	98.7

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.25	data extraction
PHASER		phasing
PARROT		phasing
ARP/wARP		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.75→45.08 Å / SU ML: 0.2115 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.5768

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2179	1695	9.87 %	0
R_work	0.178	-	-	-
obs	0.1819	17176	99.89 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 36.05 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→45.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1266	0	4	118	1388

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0079	1331
X-RAY DIFFRACTION	f_angle_d	0.8509	1816
X-RAY DIFFRACTION	f_chiral_restr	0.0483	206
X-RAY DIFFRACTION	f_plane_restr	0.0065	239
X-RAY DIFFRACTION	f_dihedral_angle_d	13.9897	825

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 (%)
1.75-1.8	0.3205	122	0.2647	1296	X-RAY DIFFRACTION	99.51
1.8-1.86	0.3171	136	0.2375	1268	X-RAY DIFFRACTION	99.86
1.86-1.93	0.2702	125	0.2143	1265	X-RAY DIFFRACTION	99.93
1.93-2	0.2446	147	0.2041	1266	X-RAY DIFFRACTION	99.93
2-2.09	0.2396	147	0.1946	1252	X-RAY DIFFRACTION	100
2.09-2.21	0.2307	158	0.1757	1248	X-RAY DIFFRACTION	99.86
2.21-2.34	0.239	133	0.1846	1295	X-RAY DIFFRACTION	99.93
2.34-2.52	0.2422	148	0.1913	1259	X-RAY DIFFRACTION	100
2.52-2.78	0.2663	154	0.1892	1288	X-RAY DIFFRACTION	99.93
2.78-3.18	0.2151	143	0.1868	1298	X-RAY DIFFRACTION	100
3.18-4.01	0.1915	144	0.1592	1332	X-RAY DIFFRACTION	100
4.01-45.08	0.1733	138	0.158	1414	X-RAY DIFFRACTION	99.74

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	7.66024167452	-3.8201962432	4.75196548826	3.98821450465	-2.8589896442	4.33815835422	-0.0261965213318	-0.473545013238	-0.252826132632	0.31205489565	0.589039026483	0.749324892536	-0.18193020895	-0.976931404034	-0.415945618507	0.176486601142	0.00630332346429	0.0600874574933	0.351182083719	0.0899254997462	0.294098931663	-16.2453175796	32.5994336078	4.49369254542
2	1.94987068809	-2.60611609303	2.60935356981	5.15450508469	-5.05054777977	5.38253578539	0.0555163942658	-0.076841324243	-0.0543996791871	-0.0336777621839	0.147182607404	0.166638779794	0.0584417463935	-0.163483735768	-0.210492025825	0.136564239928	-0.0343471653077	0.00876240532833	0.210380273101	-0.00189197012844	0.157037816137	-6.7939753738	32.515628672	1.60834811877
3	6.37370760574	-4.64497598297	3.18498336538	4.44313729018	-1.17459317422	3.02207225587	-0.10389227415	-0.209819740532	0.25246661922	0.226853918272	-0.107017809002	-0.500818362961	-0.0542329922715	0.146667180106	0.204224778562	0.253616946553	-0.045325140705	0.0113638661483	0.211895134699	0.0333008100539	0.206157375732	-1.58516285656	43.466877219	2.64372420812
4	5.92841783339	-3.87187546465	4.46004311711	2.52955198371	-2.91247772057	3.36527354914	0.277528727429	0.507894815712	0.523753016325	0.177812409303	0.0532364893844	-0.529314681864	-0.664457436083	0.727171312507	0.391943518225	0.290477037155	-0.0600135171444	-0.0184577497549	0.329317797057	-0.00188934206132	0.244055274012	7.42871005842	28.9535998627	17.341819928
5	9.24006039947	-7.35392341048	6.05742803843	8.6717453132	-6.15337921695	7.40273184678	-0.55130242933	-0.10191306351	0.388172749601	0.524662562459	0.360012106964	0.117626053539	-1.33204830179	-0.839647698396	0.072708816956	0.55377656444	0.115220414528	0.0152246104496	0.352876033262	0.019796827625	0.288016584124	-5.9696474026	38.8968591458	11.3153162421
6	4.34044242826	0.0799512619941	1.97140225346	3.35890176149	-0.803355774215	3.78056792216	-0.297890901779	-0.713685726551	0.488049735899	0.617530204712	0.512353607301	0.690134021968	-0.508263337521	-0.622504575955	-0.136209215874	0.308050862611	0.154914766294	0.0924192916092	0.473705827694	0.152613998196	0.478127210288	-21.0058964285	48.796777377	-5.83061241663
7	7.69109251111	-5.05184608052	1.70656303504	7.31814312432	-2.70106809096	4.43533442296	-0.0456663609006	0.106077182982	-0.195984575787	-0.244620994884	0.185493057433	0.320576114921	0.474696254677	0.059693034734	-0.20204415053	0.255436298323	-0.0503825282798	-0.00997013305421	0.264956469312	0.0347968032777	0.174938003538	-11.367904844	29.8686425608	-8.82607655466
8	5.17889301799	-2.93377164679	1.17848255852	9.03243904813	-2.87603270537	4.0823919993	-0.291273585764	-0.038815759953	0.501439244256	0.157936759288	-0.0177672084272	-0.809726420964	-0.658314513655	1.2774321531	0.405686470648	0.471361592061	-0.125124222441	-0.0346136536686	0.739984720142	0.00962201320654	0.256045997268	3.61976144268	30.3145284525	-1.09797722196

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 60 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 61 through 83 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 84 through 90 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 91 through 112 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 113 through 123 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 124 through 152 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 153 through 161 )

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