PDB-8ftp: FphH, Staphylococcus aureus fluorophosphonate-binding serine hydr...

ID or keywords:

Entry

Database: PDB / ID: 8ftp

Title

FphH, Staphylococcus aureus fluorophosphonate-binding serine hydrolases H, apo form

Components

Alpha/beta fold hydrolase

Keywords

HYDROLASE / FphH / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase

Function / homology

Esterase/lipase / : / Serine aminopeptidase, S33 / carboxylesterase / Serine aminopeptidase, S33 / carboxylesterase activity / Alpha/Beta hydrolase fold / Alpha/beta fold hydrolase

Function and homology information

Biological species

Staphylococcus aureus USA300-CA-263 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.37 Å

Authors

Fellner, M.

Funding support

New Zealand, 1items

Citation

Journal: Acs Infect Dis. / Year: 2023
Title: Biochemical and Cellular Characterization of the Function of Fluorophosphonate-Binding Hydrolase H (FphH) in Staphylococcus aureus Support a Role in Bacterial Stress Response.
Authors: Fellner, M. / Walsh, A. / Dela Ahator, S. / Aftab, N. / Sutherland, B. / Tan, E.W. / Bakker, A.T. / Martin, N.I. / van der Stelt, M. / Lentz, C.S.

History

Deposition	Jan 12, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 11, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 22, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8ftp.cif.gz	306.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8ftp.ent.gz	252 KB	Display	PDB format
PDBx/mmJSON format	8ftp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8ftp_validation.pdf.gz	428.2 KB	Display	wwPDB validaton report
Full document	8ftp_full_validation.pdf.gz	430.6 KB	Display
Data in XML	8ftp_validation.xml.gz	24.4 KB	Display
Data in CIF	8ftp_validation.cif.gz	37.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ft/8ftp ftp://data.pdbj.org/pub/pdb/validation_reports/ft/8ftp	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Alpha/beta fold hydrolase

B: Alpha/beta fold hydrolase

hetero molecules

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

1

A: Alpha/beta fold hydrolase

hetero molecules

defined by author
Evidence: gel filtration
28.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Alpha/beta fold hydrolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	85.149, 87.837, 164.696
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-553- HOH
2	1	B-475- HOH

#1: Protein	Alpha/beta fold hydrolase Mass: 28335.621 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus USA300-CA-263 (bacteria) Strain: USA300 / Gene: est_2 / Plasmid: pET28a-LIC / Details (production host): F1011 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D6HZA6
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.73 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.15 ul 9.1 mg/ml FphH (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 0.3 ul of reservoir solution. Sitting drop reservoir contained 200mM Calcium acetate hydrate, 100mM Tris pH 7.5, 10% ...Details: 0.15 ul 9.1 mg/ml FphH (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 0.3 ul of reservoir solution. Sitting drop reservoir contained 200mM Calcium acetate hydrate, 100mM Tris pH 7.5, 10% w/v PEG 8000 and 10% w/v PEG 1000. Crystal appeared within a day at 16C and grew until day 12.5 when it was frozen in a solution of ~25% glycerol, 75% reservoir.

Crystal

Density Matthews: 2.72 Å³/Da / Density % sol: 54.73 %

Crystal grow

Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.15 ul 9.1 mg/ml FphH (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 0.3 ul of reservoir solution. Sitting drop reservoir contained 200mM Calcium acetate hydrate, 100mM Tris pH 7.5, 10% ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 27, 2022
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.37→49.09 Å / Num. obs: 129324 / % possible obs: 99.8 % / Redundancy: 13.3 % / CC_1/2: 0.999 / R_merge(I) obs: 0.063 / R_pim(I) all: 0.018 / R_rim(I) all: 0.066 / Χ²: 1.01 / Net I/σ(I): 18.9 / Num. measured all: 1722894
Reflection shell	Resolution: 1.37→1.39 Å / % possible obs: 97.3 % / Redundancy: 13.2 % / R_merge(I) obs: 1.539 / Num. measured all: 81791 / Num. unique obs: 6219 / CC_1/2: 0.641 / R_pim(I) all: 0.434 / R_rim(I) all: 1.6 / Χ²: 1 / Net I/σ(I) obs: 1.9

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1-4487	refinement
Aimless	0.7.8	data scaling
XDS		data reduction
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.37→40.85 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.62 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1643	6495	5.03 %
R_work	0.1532	-	-
obs	0.1537	129253	99.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.37→40.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3918	0	8	541	4467

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009
X-RAY DIFFRACTION	f_angle_d	1.028
X-RAY DIFFRACTION	f_dihedral_angle_d	15.566	1524
X-RAY DIFFRACTION	f_chiral_restr	0.08	575
X-RAY DIFFRACTION	f_plane_restr	0.007	733

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 (%)
1.37-1.38	0.3159	200	0.2859	3914	X-RAY DIFFRACTION	96
1.38-1.4	0.234	232	0.2371	4006	X-RAY DIFFRACTION	100
1.4-1.42	0.2479	218	0.2356	4107	X-RAY DIFFRACTION	100
1.42-1.44	0.2369	215	0.2168	4032	X-RAY DIFFRACTION	100
1.44-1.45	0.2088	226	0.2047	4076	X-RAY DIFFRACTION	100
1.45-1.47	0.2341	190	0.1922	4059	X-RAY DIFFRACTION	100
1.47-1.5	0.2178	204	0.1784	4100	X-RAY DIFFRACTION	100
1.5-1.52	0.1669	200	0.1751	4073	X-RAY DIFFRACTION	100
1.52-1.54	0.1867	189	0.1728	4100	X-RAY DIFFRACTION	100
1.54-1.57	0.1916	205	0.1724	4104	X-RAY DIFFRACTION	100
1.57-1.59	0.1814	245	0.1648	4004	X-RAY DIFFRACTION	100
1.59-1.62	0.1965	186	0.163	4103	X-RAY DIFFRACTION	100
1.62-1.65	0.1902	224	0.1555	4112	X-RAY DIFFRACTION	100
1.65-1.69	0.1608	231	0.1542	4037	X-RAY DIFFRACTION	100
1.69-1.72	0.1425	253	0.1498	4024	X-RAY DIFFRACTION	100
1.72-1.76	0.1771	225	0.1498	4054	X-RAY DIFFRACTION	100
1.76-1.81	0.1563	197	0.1481	4131	X-RAY DIFFRACTION	100
1.81-1.86	0.1698	230	0.1499	4087	X-RAY DIFFRACTION	100
1.86-1.91	0.1607	202	0.1487	4107	X-RAY DIFFRACTION	100
1.91-1.97	0.1755	239	0.1507	4091	X-RAY DIFFRACTION	100
1.97-2.04	0.1756	221	0.1505	4068	X-RAY DIFFRACTION	100
2.04-2.13	0.1501	202	0.1467	4101	X-RAY DIFFRACTION	100
2.13-2.22	0.1636	185	0.144	4132	X-RAY DIFFRACTION	100
2.22-2.34	0.1326	220	0.146	4126	X-RAY DIFFRACTION	100
2.34-2.49	0.1642	242	0.1465	4059	X-RAY DIFFRACTION	100
2.49-2.68	0.165	233	0.1501	4135	X-RAY DIFFRACTION	100
2.68-2.95	0.1538	239	0.1514	4129	X-RAY DIFFRACTION	100
2.95-3.38	0.1705	220	0.1511	4179	X-RAY DIFFRACTION	100
3.38-4.25	0.1551	199	0.1343	4199	X-RAY DIFFRACTION	100
4.25-40.85	0.1534	223	0.1599	4309	X-RAY DIFFRACTION	99

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	4.5021	1.2185	1.7092	4.6883	0.783	4.5759	-0.2273	0.3849	0.4375	-0.3301	0.0189	0.2125	-0.3581	-0.1021	0.2053	0.1728	0.0644	-0.0002	0.149	0.0153	0.1469	-8.4727	-13.4607	17.6619
2	1.6831	-0.4538	0.3419	1.3517	-0.1031	1.7552	0.0524	0.1406	-0.1125	-0.1122	-0.0306	0.069	0.0931	-0.1289	-0.0185	0.1443	0.019	-0.0124	0.1531	-0.0105	0.1371	-7.4177	-25.3155	19.5287
3	5.0415	-0.0577	2.7125	0.5951	-0.043	2.7186	0.1527	0.2613	-0.4041	-0.0568	0.0154	0.2573	0.1926	-0.2329	-0.2357	0.2403	-0.0452	-0.0254	0.2841	-0.0327	0.3229	-21.8827	-36.7275	13.9159
4	2.899	-0.6631	0.6929	3.0805	-0.3872	2.5006	-0.0312	-0.1155	-0.052	0.1315	0.0887	0.1997	0.0026	-0.3224	-0.0524	0.1393	0.0139	0.0133	0.1965	0.004	0.1023	-9.1949	-26.699	34.5143
5	3.9838	0.5453	0.38	4.4379	1.6198	3.6599	-0.0336	-0.434	0.13	0.4442	-0.0427	0.2912	-0.0333	-0.2871	0.0781	0.1909	0.0577	0.0065	0.1956	-0.0264	0.1899	-29.6963	8.6612	23.4956
6	2.6283	0.0799	-0.012	2.2978	0.5057	1.7854	-0.0652	-0.2943	0.2422	0.2969	0.1369	-0.1731	-0.1605	0.1544	0.0096	0.201	0.0402	-0.0239	0.1708	-0.0663	0.1561	-20.8827	12.3154	23.2337
7	4.2144	0.3771	-0.0375	2.9816	0.3737	2.1546	-0.1373	-0.5091	-0.1112	0.4035	0.1476	0.039	0.1476	0.0697	-0.0128	0.2363	0.0839	0.0004	0.193	0.0108	0.1426	-19.9731	0.1171	25.872
8	2.2649	-0.4428	-0.4546	2.793	-0.2693	2.8234	-0.0416	-0.1672	0.2029	0.0988	0.0402	-0.2786	-0.15	0.2657	-0.0257	0.15	0.0218	-0.0224	0.1537	-0.0337	0.1665	-11.9335	5.4637	16.544
9	2.4265	0.2728	-1.3624	1.4196	0.672	2.2991	0.1835	-0.3404	0.8471	0.0483	0.103	-0.1618	-0.582	0.2569	0.0895	0.4521	-0.094	-0.0339	0.3906	-0.2721	0.7407	-9.9222	26.4659	26.8589
10	0.7079	-0.5982	-0.5254	1.1316	0.5632	0.4122	0.1059	-0.5219	0.6478	0.3294	0.2869	-0.6306	-0.2357	0.4331	0.18	0.6137	-0.0817	-0.1162	0.685	-0.5186	1.0278	-7.3761	31.1838	35.5227
11	1.5023	0.8059	0.6535	3.8734	2.256	3.6286	-0.0771	-0.5378	0.3593	0.3282	0.2757	-0.6185	-0.0024	0.6043	-0.2587	0.2074	0.02	-0.0819	0.412	-0.1324	0.3742	-1.3459	7.0907	21.178
12	2.9069	-0.7946	-0.3448	3.0618	0.603	2.6377	0.0467	0.0466	0.3054	-0.1327	0.0247	-0.2764	-0.2532	0.2115	-0.083	0.1665	-0.0055	0.0113	0.1389	-0.0025	0.1693	-10.3742	7.945	5.9405
13	3.8626	-0.3059	-1.2277	1.6319	1.2398	2.42	0.1419	0.1931	0.8204	-0.2578	0.0272	-0.2375	-0.694	-0.0371	-0.1281	0.4067	0.0195	0.0335	0.2008	0.0293	0.3644	-18.0199	20.8276	8.9018
14	3.9676	-0.5753	-0.456	5.7001	0.7044	3.5846	0.0205	0.2475	-0.0663	-0.3205	-0.065	0.2701	-0.0426	-0.2758	0.1004	0.1592	0.0406	-0.0276	0.1603	-0.0292	0.1495	-26.365	5.5107	6.7125

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 16 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 124 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 125 through 177 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 178 through 246 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 4 through 16 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 17 through 64 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 65 through 86 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 87 through 124 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 125 through 140 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 141 through 157 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 158 through 177 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 178 through 215 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 216 through 227 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 228 through 246 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi