PDB-7mqw: Histidine triad protein

ID or keywords:

Entry

Database: PDB / ID: 7mqw

Title

Histidine triad protein

Components

HIT family protein

Keywords

UNKNOWN FUNCTION / Histidine triad protein

Function / homology

Histidine triad (HIT) protein / HIT domain / HIT domain profile. / HIT-like domain / HIT-like superfamily / catalytic activity / HIT family protein

Function and homology information

Biological species

Mycolicibacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Ghosh, S. / Goldgur, Y. / Shuman, S.

Funding support

United States, 1items

Citation

Journal: Unpublished
Title: Histidine triad protein
Authors: Ghosh, S. / Goldgur, Y. / Shuman, S.

History

Deposition	May 6, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 26, 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	7mqw.cif.gz	154.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7mqw.ent.gz	99.6 KB	Display	PDB format
PDBx/mmJSON format	7mqw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7mqw_validation.pdf.gz	437.6 KB	Display	wwPDB validaton report
Full document	7mqw_full_validation.pdf.gz	438.5 KB	Display
Data in XML	7mqw_validation.xml.gz	16 KB	Display
Data in CIF	7mqw_validation.cif.gz	23.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mq/7mqw ftp://data.pdbj.org/pub/pdb/validation_reports/mq/7mqw	HTTPS FTP

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Related structure data

Related structure data	3p0tS S: Starting model for refinement
Similar structure data	3p0t-d 2qlt-d 5u8k-1 1428 1dzw-d 3i24-d 1byr-1 6upd-2 1rlm-1 1xqp-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (1) #245 - May 2020 Spliceosomes similarity (1) #86 - Feb 2007 Exosomes similarity (1)

Deposited unit

A: HIT family protein

B: HIT family protein

hetero molecules

31.6 kDa, 2 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)	55.149, 55.149, 205.735
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2
Space group name Hall	P4nw2abw
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+3/4 #3: y+1/2,-x+1/2,z+1/4 #4: x+1/2,-y+1/2,-z+1/4 #5: -x+1/2,y+1/2,-z+3/4 #6: -x,-y,z+1/2 #7: y,x,-z #8: -y,-x,-z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	B-342- HOH

#1: Protein	HIT family protein / Histidine triad protein Mass: 15634.880 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: hit_2, ERS451418_05688 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0D6J0U7
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.5 Å³/Da / Density % sol: 50.83 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 15.6 mg/mL (1mM) protein + 5 mM ATP in 0.2 M ammonium sulfate, 30% w/v PEG4000 Temp details: ambient

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 4, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.55→50 Å / Num. obs: 47498 / % possible obs: 99.9 % / Redundancy: 11.7 % / B_iso Wilson estimate: 18.07 Å² / CC_1/2: 0.998 / R_pim(I) all: 0.024 / Net I/σ(I): 41.3
Reflection shell	Resolution: 1.55→1.58 Å / Num. unique obs: 2314 / CC_1/2: 0.861 / R_pim(I) all: 0.281

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Processing

Software

Name	Version	Classification
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing
PHENIX	1.19.1_4122	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3P0T

3p0t

Resolution: 1.55→48.6 Å / SU ML: 0.1719 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1012
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2064	2271	4.79 %
R_work	0.1799	45093	-
obs	0.1812	47364	99.88 %

Solvent computation

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

Displacement parameters

B_iso mean: 23.43 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→48.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2134	0	15	345	2494

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0063	2190
X-RAY DIFFRACTION	f_angle_d	0.884	2978
X-RAY DIFFRACTION	f_chiral_restr	0.0545	342
X-RAY DIFFRACTION	f_plane_restr	0.0078	390
X-RAY DIFFRACTION	f_dihedral_angle_d	5.8328	288

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 (%)
1.55-1.58	0.327	123	0.3164	2740	X-RAY DIFFRACTION	98.79
1.58-1.62	0.2598	140	0.2607	2773	X-RAY DIFFRACTION	99.93
1.62-1.66	0.2496	136	0.2255	2751	X-RAY DIFFRACTION	99.9
1.66-1.71	0.2539	149	0.2062	2748	X-RAY DIFFRACTION	99.93
1.71-1.76	0.232	144	0.1866	2759	X-RAY DIFFRACTION	99.86
1.76-1.81	0.2001	124	0.1881	2801	X-RAY DIFFRACTION	100
1.81-1.88	0.1892	135	0.195	2771	X-RAY DIFFRACTION	99.9
1.88-1.95	0.2274	125	0.2057	2821	X-RAY DIFFRACTION	100
1.95-2.04	0.1667	161	0.18	2772	X-RAY DIFFRACTION	99.9
2.04-2.15	0.222	150	0.1772	2778	X-RAY DIFFRACTION	100
2.15-2.28	0.2058	147	0.1703	2820	X-RAY DIFFRACTION	99.97
2.28-2.46	0.1923	145	0.1754	2812	X-RAY DIFFRACTION	100
2.46-2.71	0.2056	150	0.1726	2832	X-RAY DIFFRACTION	99.97
2.71-3.1	0.1959	137	0.1858	2894	X-RAY DIFFRACTION	100
3.1-3.9	0.1968	161	0.1572	2902	X-RAY DIFFRACTION	99.97
3.9-48.6	0.2075	144	0.1681	3119	X-RAY DIFFRACTION	99.94

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	0.111668334243	0.106598792567	0.195667774034	0.0927469279236	0.171443506945	0.347983036146	-0.302307203443	0.0687681703133	-0.329281656826	-0.0727857278044	-0.15838309927	-0.440408978866	0.424396791504	0.0108377529684	-0.10334678147	0.512599751586	-0.0313951037778	0.10854143504	0.176195078144	0.0515306849938	0.341955326745	21.4047645125	-20.5744484517	17.9231698335
2	0.0521497832265	0.0106599032364	-0.0731547488254	0.0873745946802	0.0423631522246	0.10645245206	0.0011564493504	0.118620109073	-0.307024522249	-0.252733066171	-0.0284402539768	0.123762337561	0.559446929125	-0.355458567672	0.000483483455282	0.345510687806	-0.0969468979177	-0.00525039818804	0.234125445429	0.0377321752496	0.306915608644	17.2006974551	-18.2113230319	25.4343018224
3	0.288087350685	0.30065860673	-0.201123190656	0.40983944337	-0.404663436312	0.476393912285	0.0669045492413	0.0573965327418	-0.0032236222422	-0.0172400031894	-0.0152877754131	0.043603285682	-0.00430739230194	-0.0790056305652	-1.48411192939E-6	0.107886874394	-0.0234209737207	-0.00836004537041	0.149936624997	0.013010693338	0.139514424015	23.0673056636	-8.33650003072	22.5082320543
4	0.279461903732	-0.064901898312	-0.32234928005	0.270408342476	0.0787284079546	0.259616781942	-0.041645798022	0.100855751893	0.0773354986327	-0.0335993169603	0.0675885009095	0.0354035852022	0.0760675796685	-0.281217214521	0.00966038480182	0.121466935925	-0.0568966957716	-0.0214382199828	0.199635989922	0.0245362579123	0.143707774433	19.4201175317	-7.7849032838	9.33792123441
5	0.562514906746	0.326962924743	-0.316742959512	0.263173484367	-0.147267752619	0.643880735494	0.248622591924	0.116185662548	0.175492320166	0.136794713708	-0.0435183361857	-0.00708979810318	-0.616151132368	-0.148004257517	0.0352734175102	0.194468148271	0.075601697649	0.0436376773289	0.205842307086	0.0291747401331	0.14656045629	23.1198960572	1.47852387365	18.4077784891
6	0.148375499663	-0.135774937025	-0.0362360911753	0.148156160723	-0.0623273095064	0.159060696541	0.190792216109	-0.175077447646	0.117955751348	0.233533644251	-0.261499027883	0.141292030201	-0.153484207368	-0.179782253139	0.00859917962647	0.198192588302	-0.0722401649561	0.00840782576391	0.169552361428	-0.0277965368699	0.137531601565	34.4695240597	1.92751004489	20.7943914054
7	-0.0110195793042	0.127471292264	0.0116660947094	0.0440182840956	-0.0249976803009	0.303277854063	-0.0159457442104	-0.184127039346	-0.0805448691602	-0.0478943769145	-0.0719871619226	-0.0453910882051	0.0292865589256	-0.00245025899145	-0.00176881735211	0.122696634852	-0.0226902089415	-0.00976145547218	0.127661945186	0.00701105817274	0.138876355734	31.1402846509	-8.18749188632	15.3149104227
8	0.00581684428636	0.0236631804536	0.024462706109	0.0503113069034	0.0136460832765	0.0189725903529	-0.202775091746	-0.135779624872	-0.0411292899236	-0.287461075067	0.195530140314	-0.218053686617	0.0426948326878	0.507263291083	0.000260902254875	0.23345981528	0.0328532338902	0.0544976673516	0.270671637254	0.0742972337618	0.292455066345	38.6575368078	-10.77051612	15.4736151158
9	0.104607817614	0.0139757755159	-0.0885762890009	0.547177236601	-0.22792793687	0.54198930014	-0.0215177945916	-0.0105795076383	0.0495572213051	0.160388127627	-0.0579286196833	-0.116746375665	-0.0541672179992	-0.0206941728977	-4.57007435751E-5	0.152213115177	-0.0189429578655	0.00827128479788	0.163767743745	0.0106287579774	0.143590620391	27.5421770673	-7.05800440804	30.3237741415
10	0.241136449762	0.105067279214	-0.156754926679	0.104542605758	-0.127298718565	0.19423503029	0.149773752546	-0.262850935685	-0.177789274548	0.0938004896414	-0.177027805157	-0.17790498476	-0.0356588258265	0.255853350813	-0.0376565842027	0.16646604614	-0.0878815548077	-0.0180922094234	0.196390711201	0.0433891305383	0.173162384966	44.9092105528	11.3999258582	1.35904905905
11	0.395999643681	0.113009617823	-0.420701396592	0.38990907999	-0.660529495819	0.904737083306	0.0922768358424	-0.00544458913901	0.0816484253488	0.0804747580286	-0.0252775870962	0.0414905445148	-0.202604426297	0.0284549607495	-0.00297001047917	0.164925270475	-0.00169124672045	0.00590273630054	0.0904541261123	0.00574162838549	0.150331418007	33.6835352984	7.20259078722	4.1396032301
12	0.610343181552	0.451578609661	0.0346950435659	0.549409648939	-0.324553023968	0.425888260613	0.0208348946136	0.0282270404529	0.020290116847	0.0950344288356	-0.0615997559952	0.135342190099	0.0325654865066	-0.386495066542	0.000127943124003	0.149066886664	-0.00428867982844	-0.0117512549323	0.186112704503	0.0252652626349	0.156010031375	25.7760302093	1.75963769708	1.51890706161
13	0.290058788339	0.346770823519	-0.107755580255	0.191881754171	-0.249149745794	0.371644798204	-0.0562355537014	-0.0103246933874	-0.0230374064	-0.132463026213	0.00288668184368	-0.040344495633	-0.076558440833	0.0120373120576	-0.0557716267401	0.14069498904	-0.0334778441283	-0.0122149829968	0.0995155925651	0.00645748038126	0.13777784381	34.3276521519	-1.37445019468	6.41976453533
14	0.0873903368601	0.0893248151484	0.0664213465664	0.17951456408	-0.079942587457	-0.0362960753613	-0.0501218296667	0.431403508206	0.00510036768344	0.211477062712	0.128795986699	0.147343887819	0.203860547917	0.159417643919	0.0073721250911	0.129808960234	0.0148593166615	0.00238745599648	0.227798186	0.0322036315388	0.187448407052	43.1307562791	-7.82628652405	4.14003437047
15	0.118426913841	0.100858533723	0.122384060226	0.409876882749	-0.276781566676	0.74827268014	0.0270411453209	0.192662118891	0.140791841667	-0.0820467165388	-0.0234610774113	0.0333121878266	-0.0185489224654	0.0945255700521	1.81099163554E-5	0.138933573387	-0.00874015868989	-0.024601459275	0.156480555558	0.0200617264626	0.128643363624	33.896402443	0.286461506953	-10.49671367

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 13 )	A	A	3 - 13	1 - 11
2	2	chain 'A' and (resid 14 through 20 )	A	A	14 - 20	12 - 18
3	3	chain 'A' and (resid 21 through 41 )	A	A	21 - 41	19 - 39
4	4	chain 'A' and (resid 42 through 57 )	A	A	42 - 57	40 - 55
5	5	chain 'A' and (resid 58 through 79 )	A	A	58 - 79	56 - 77
6	6	chain 'A' and (resid 80 through 87 )	A	A	80 - 87	78 - 85
7	7	chain 'A' and (resid 88 through 108 )	A	A	88 - 108	86 - 106
8	8	chain 'A' and (resid 109 through 113 )	A	A	109 - 113	107 - 111
9	9	chain 'A' and (resid 114 through 139 )	A	A	114 - 139	112 - 137
10	10	chain 'B' and (resid 3 through 20 )	B	B	3 - 20	1 - 18
11	11	chain 'B' and (resid 21 through 57 )	B	B	21 - 57	19 - 55
12	12	chain 'B' and (resid 58 through 79 )	B	B	58 - 79	56 - 77
13	13	chain 'B' and (resid 80 through 103 )	B	B	80 - 103	78 - 101
14	14	chain 'B' and (resid 104 through 119 )	B	B	104 - 119	102 - 117
15	15	chain 'B' and (resid 120 through 139 )	B	B	120 - 139	118 - 137

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