PDB-8zf2: Quorum Sensing master regulator HapR of Photobacterium marinum

ID or keywords:

Entry

Database: PDB / ID: 8zf2

Title

Quorum Sensing master regulator HapR of Photobacterium marinum

Components

Quorum-sensing regulator of virulence HapR

Keywords

TRANSCRIPTION / Master regulator. HapR / DNA Binding

Function / homology

Function and homology information

transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function

Biological species

Photobacterium marinum (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Basu Choudhury, G. / Saha, A. / Datta, S. / Ray Chaudhuri, S.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Quorum Sensing master regulator HapR of Photobacterium marinum
Authors: Basu Choudhury, G. / Saha, A. / Datta, S. / Ray Chaudhuri, S.

History

Deposition	May 7, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 7, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8zf2.cif.gz	209.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8zf2.ent.gz	138.2 KB	Display	PDB format
PDBx/mmJSON format	8zf2.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/zf/8zf2 ftp://data.pdbj.org/pub/pdb/validation_reports/zf/8zf2	HTTPS FTP

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Related structure data

Related structure data	7xxoS S: Starting model for refinement
Similar structure data	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

Deposited unit

A: Quorum-sensing regulator of virulence HapR

B: Quorum-sensing regulator of virulence HapR

hetero molecules

46.7 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)	40.600, 44.310, 61.026
Angle α, β, γ (deg.)	70.390, 72.780, 85.110
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#1: Protein	Quorum-sensing regulator of virulence HapR Mass: 23223.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photobacterium marinum (bacteria) / Gene: C942_04851 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: L8JC63
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.26 Å³/Da / Density % sol: 45.64 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion Details: 20% PEG 3350, Sodium Citrate pH 4.0, 200 mM Sodium citrate tribasic

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54 Å
Detector	Type: Bruker PHOTON III / Detector: PIXEL / Date: Dec 14, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.8→55.13 Å / Num. obs: 35478 / % possible obs: 100 % / Redundancy: 8.8 % / B_iso Wilson estimate: 20.63 Å² / CC_1/2: 0.999 / Net I/σ(I): 17.4
Reflection shell	Resolution: 1.8→1.86 Å / Num. unique obs: 3559 / CC_1/2: 0.701

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
PROTEUM		data scaling
PROTEUM		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7XXO

7xxo

Resolution: 1.8→26.04 Å / SU ML: 0.243 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 24.5938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2289	1905	5.65 %
R_work	0.188	31832	-
obs	0.1903	33737	95.12 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 23.92 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→26.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3065	0	14	416	3495

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3150
X-RAY DIFFRACTION	f_angle_d	0.6548	4271
X-RAY DIFFRACTION	f_chiral_restr	0.0402	472
X-RAY DIFFRACTION	f_plane_restr	0.0076	554
X-RAY DIFFRACTION	f_dihedral_angle_d	4.2696	417

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 (%)
1.8-1.85	0.4338	111	0.3304	1907	X-RAY DIFFRACTION	78.25
1.85-1.89	0.3438	121	0.2831	2017	X-RAY DIFFRACTION	85.21
1.9-1.95	0.2978	131	0.2408	2140	X-RAY DIFFRACTION	89.8
1.95-2.01	0.2769	135	0.2156	2222	X-RAY DIFFRACTION	92.65
2.01-2.09	0.2703	136	0.2097	2238	X-RAY DIFFRACTION	94.77
2.09-2.17	0.2372	139	0.1912	2322	X-RAY DIFFRACTION	97
2.17-2.27	0.2264	139	0.181	2339	X-RAY DIFFRACTION	98.22
2.27-2.39	0.2427	141	0.1811	2370	X-RAY DIFFRACTION	99.05
2.39-2.54	0.2328	143	0.1891	2387	X-RAY DIFFRACTION	99.02
2.54-2.73	0.2608	141	0.1848	2356	X-RAY DIFFRACTION	99.09
2.73-3.01	0.2274	141	0.1906	2366	X-RAY DIFFRACTION	99.48
3.01-3.44	0.2069	144	0.1816	2411	X-RAY DIFFRACTION	99.84
3.44-4.33	0.1892	141	0.1638	2369	X-RAY DIFFRACTION	99.8
4.33-26.04	0.1935	142	0.1695	2388	X-RAY DIFFRACTION	99.8

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	1.79996799919	-0.188157112178	-0.865362954682	4.22662708539	2.00349704508	2.90834315413	0.143955063279	0.0640372606477	-0.171273235541	0.0876915371477	-0.0747958857506	-0.170388230195	-0.0572345066597	0.0854419297684	-0.0709250329696	0.179100243871	-0.0332337880437	-0.0256193939602	0.168876396068	-0.00732049073704	0.1259234448	13.7899069198	10.5811271161	27.2146742505
2	2.52198209812	0.115412387328	0.173864215299	2.98143604901	0.351658150293	2.97654345209	-0.117943649879	0.184810727587	-0.193837232024	0.353800911643	0.137641705136	-0.0850807495756	0.20531099601	0.103078306226	0.00962364399147	0.228204590519	0.00022606263517	-5.06928882875E-5	0.227474638602	-0.0207545292943	0.126494410485	13.4291190118	12.3143793399	36.0161938083
3	1.25665151361	0.198781519128	1.02903706189	1.75377684129	1.47292346071	8.27783818989	0.236406380826	-0.0547455381016	-0.0375416532962	0.0646831770145	0.00481637183497	-0.00208477233932	0.0753115314373	-0.249218358657	-0.212621989118	0.164820028788	0.00832036254814	0.00472371191828	0.163992270464	0.0137940426935	0.239900929847	5.57551610787	3.83021290807	18.6488860535
4	2.45839585581	0.559360753554	1.27877933407	1.46723377298	1.28634761932	2.54188625089	-0.226124845762	0.0299072266814	0.382001994977	-0.337086580063	0.0112642193386	0.0266295656674	-0.286457564119	-0.269401542722	0.184984464511	0.167386164701	0.0127872138099	0.00616844411993	0.136690297058	0.0496612617766	0.18365628356	7.66824283919	2.45127191214	0.301978801715
5	2.7516149105	0.0155291936673	-0.79415855588	4.95442128026	-0.427472802191	2.11848208066	0.0334320550789	-0.188033230456	0.127739096452	0.407055579113	-0.0548568131701	-0.277043709505	-0.112843797091	0.175965741568	0.0561438501465	0.14172888372	0.0206438521916	-0.0518627487582	0.169433756064	-0.0476651921612	0.190774913698	13.1346099264	-2.38207110137	19.5770654369
6	1.69897250907	0.180728713008	0.814336340206	1.24052251791	-0.0881593068764	4.89684541746	0.00450934943222	-0.0599397678561	0.0923573157077	-0.0608879485922	0.00841684874894	0.0648861542731	-0.054589356122	-0.377846034755	0.0157344002806	0.114839643159	-0.0112498975097	0.000668911478418	0.155713453877	0.0224273145841	0.180409809217	-0.90742750328	-7.59261818073	6.56976603759
7	4.42176713728	0.782491732845	0.704305242808	1.01277860631	0.250974004028	0.868837098516	0.0286557892914	-0.0173460601643	-0.0612247328291	-0.0691545904979	-0.00959067749147	-0.0874493863348	0.0219791911445	0.0124440010012	-0.0179063592542	0.113452070228	0.0179874905585	-0.000363585449303	0.100916049261	0.0438679596415	0.135742878428	11.8999822553	-8.2465846863	7.03296543257
8	3.19855570281	0.500160076082	1.11517243689	1.87813209619	1.09817306271	1.66354338328	0.0157461565474	0.289100501731	-0.0897890937909	-0.291405527721	0.0440807011902	-0.238765326863	-0.0644579189249	0.0861999589647	-0.0497888935198	0.193246564197	-0.00619912474528	0.027381566581	0.165724107495	0.0356124037398	0.212434619349	17.4174250033	-3.10078097267	-2.50054875371
9	5.3791186706	-1.73315714734	0.585020767082	2.55674310491	-0.962483502783	2.68933599106	-0.0506739113222	-0.310058799106	-0.442531219036	0.273778582864	-0.0298680380926	0.0816692619567	0.319407802926	-0.120048327483	0.0696341827049	0.227796431295	-0.0444885478037	-0.00310443980362	0.201740649383	0.00426048012728	0.145927997217	27.884744766	-20.6980407871	33.677949404
10	0.38051390546	-0.0451558793859	1.05503568591	0.981619714843	0.188022050178	2.98829172532	-0.0768394052462	-0.124355268397	-0.0534488156012	0.269718941368	0.0408518667075	-0.00772512000501	-0.0520330873683	-0.214719527428	0.00396683941062	0.238139878682	-0.00266537431462	-0.0220722876469	0.266727197783	-0.0221718561574	0.185470630904	30.5181585315	-13.8193772599	38.1237138226
11	1.86392786784	1.82707892637	2.44421335056	3.72489845058	3.24759785844	4.91185379975	-0.136660037775	0.0808576250039	-0.0538066816693	-0.0365761048147	0.249118281865	-0.00967963172898	-0.076185095383	0.285301579126	-0.0969959955932	0.123828383891	0.0178610414557	-0.00288415502699	0.159646446908	0.0131918419827	0.153141952938	27.5148840124	-19.3099343902	19.9090436794
12	0.409734939341	0.130641919099	0.115941028475	1.4560287054	0.586268652441	3.41619186089	-0.00160278987959	0.120619032284	-0.1627737055	0.0467742501889	0.101224020638	-0.00911563085362	0.343664355482	-0.0295392312736	-0.107874280759	0.149868415072	-0.00516481674358	-0.000986255966852	0.121639927292	-0.0032180086169	0.180642931845	16.219368838	-28.5009271594	8.56194179499
13	2.25285574395	2.31498251162	-0.308511740437	4.48947018014	-1.02547760575	1.61808289316	0.0573808729377	-0.0160358011487	0.0242031548974	0.22732224537	-0.0359617553583	0.0614243064734	-0.0167112204355	-0.0162091089862	-0.0376019897739	0.0954577043663	0.0227316703529	-0.000430131389989	0.113134979194	-0.0099484303333	0.0882692806112	18.499675631	-16.5844692394	21.2107294679
14	4.1497076226	-1.62942685553	-1.00204678828	3.23415775534	-0.384622937968	2.27987181777	-0.000829725251783	-0.340585339088	0.487488226975	0.352984787731	-0.0477467278243	-0.291904959851	-0.150543179195	0.0205418644443	0.047930372329	0.151830071137	-0.0122253206795	-0.0134211005306	0.226852013281	-0.0431400676813	0.204810982742	27.9480094284	-7.63256767024	17.2744200312
15	2.42294916746	0.759464320515	0.107681409185	2.98813628114	1.31677741574	4.16136525314	-0.0622875851144	0.369600279895	-0.0733908982954	-0.314334631636	0.188302224726	-0.201266654979	-0.00460341315522	0.0861359453278	-0.129364060407	0.173805560125	-0.0280749581846	0.051120707668	0.157325214572	-7.255900362E-5	0.132747800544	22.9465903344	-21.4202570559	-2.08382974363
16	2.44289411091	-0.330847626197	-1.30956682739	1.33003868776	1.01911532623	3.34657005344	0.0526552678412	0.0380963914832	0.0774076109382	-0.174283253505	-0.0766108959641	0.0943973828768	-0.160435507115	-0.148649006305	-0.0231161703413	0.120483715722	0.00361415022657	0.00421492493408	0.0624794951752	0.0109912659341	0.141099100792	13.9845674104	-15.4033511846	8.92167289528
17	4.78604875573	-0.414691523589	-1.59544967396	3.55414474981	0.0730830314631	5.68234553959	0.0665898334846	0.13835912786	-0.324089150834	0.244393906598	-0.0532816621291	0.290564902667	0.365233814258	-0.787916815994	-0.0471299268163	0.207512096655	-0.0581917125429	-0.00228566033705	0.250268389641	-0.0414801618551	0.261636387581	5.70882907981	-23.8023088273	7.79839170505

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 12 through 38 )	A	A	12 - 38	1 - 27
2	2	chain 'A' and (resid 39 through 59 )	A	A	39 - 59	28 - 48
3	3	chain 'A' and (resid 60 through 83 )	A	A	60 - 83	49 - 72
4	4	chain 'A' and (resid 84 through 106 )	A	A	84 - 106	73 - 95
5	5	chain 'A' and (resid 107 through 126 )	A	A	107 - 126	96 - 115
6	6	chain 'A' and (resid 127 through 159 )	A	A	127 - 159	116 - 148
7	7	chain 'A' and (resid 160 through 180 )	A	A	160 - 180	149 - 169
8	8	chain 'A' and (resid 181 through 200 )	A	A	181 - 200	170 - 189
9	9	chain 'B' and (resid 12 through 32 )	B	C	12 - 32	1 - 21
10	10	chain 'B' and (resid 33 through 59 )	B	C	33 - 59	22 - 48
11	11	chain 'B' and (resid 60 through 83 )	B	C	60 - 83	49 - 72
12	12	chain 'B' and (resid 84 through 106 )	B	C	84 - 106	73 - 95
13	13	chain 'B' and (resid 107 through 120 )	B	C	107 - 120	96 - 109
14	14	chain 'B' and (resid 121 through 134 )	B	C	121 - 134	110 - 123
15	15	chain 'B' and (resid 135 through 159 )	B	C	135 - 159	124 - 148
16	16	chain 'B' and (resid 160 through 180 )	B	C	160 - 180	149 - 169
17	17	chain 'B' and (resid 181 through 201 )	B	C	181 - 201	170 - 190

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