PDB-9bpw: Crystal Structure of Fumarate Hydratase FumC from Staphylococcus ...

ID or keywords:

Entry

Database: PDB / ID: 9bpw

Title

Crystal Structure of Fumarate Hydratase FumC from Staphylococcus aureus

Components

Fumarate hydratase class II

Keywords

HYDROLASE / Hydratase / Fumarase / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID

Function / homology

Function and homology information

fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function

Biological species

Staphylococcus aureus subsp. aureus USA300_FPR3757 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Kim, Y. / Tesar, C. / Endres, M. / Babnigg, G. / Wong, T. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of Fumarate Hydratase FumC from Staphylococcus aureus
Authors: Kim, Y. / Tesar, C. / Endres, M. / Babnigg, G. / Wong, T. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)

History

Deposition	May 8, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 14, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9bpw.cif.gz	880.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9bpw.ent.gz	612.4 KB	Display	PDB format
PDBx/mmJSON format	9bpw.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/bp/9bpw ftp://data.pdbj.org/pub/pdb/validation_reports/bp/9bpw	HTTPS FTP

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Related structure data

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
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (11) #127 - Jul 2010 Crystallins similarity (7)

Deposited unit

A: Fumarate hydratase class II

B: Fumarate hydratase class II

C: Fumarate hydratase class II

D: Fumarate hydratase class II

hetero molecules

207 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	243.865, 108.891, 109.023
Angle α, β, γ (deg.)	90.000, 116.620, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Fumarate hydratase class II / Fumarase C / Aerobic fumarase / Iron-independent fumarase Mass: 51164.656 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300_FPR3757 (bacteria) Gene: fumC / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q5HES4, fumarate hydratase

#1: Protein

Fumarate hydratase class II / Fumarase C / Aerobic fumarase / Iron-independent fumarase

Mass: 51164.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Staphylococcus aureus subsp. aureus USA300_FPR3757 (bacteria)
Gene: fumC / Plasmid: pMCSG53 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q5HES4, fumarate hydratase

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Non-polymers , 5 types, 612 molecules

#2: Chemical	ChemComp-FUM / FUMARIC ACID Mass: 116.072 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₄O₄
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	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: 3.16 Å³/Da / Density % sol: 61.1 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M lithium citrate, 20 % w/v PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 165261 / % possible obs: 96.2 % / Redundancy: 7 % / B_iso Wilson estimate: 34.07 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.134 / R_pim(I) all: 0.055 / R_rim(I) all: 0.145 / Net I/σ(I): 16.1
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 7 % / R_merge(I) obs: 2.182 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 8220 / CC_1/2: 0.545 / R_pim(I) all: 0.877 / R_rim(I) all: 2.355 / % possible all: 96.5

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→48.73 Å / SU ML: 0.2696 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.6332
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2151	7752	4.79 %	rsndom
R_work	0.1838	153936	-	-
obs	0.1853	161688	93.99 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 47.54 Å²

Refinement step

Cycle: LAST / Resolution: 2→48.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14360	0	138	582	15080

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	14956
X-RAY DIFFRACTION	f_angle_d	0.7045	20291
X-RAY DIFFRACTION	f_chiral_restr	0.0453	2237
X-RAY DIFFRACTION	f_plane_restr	0.0055	2663
X-RAY DIFFRACTION	f_dihedral_angle_d	14.007	5525

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 (%)
2-2.02	0.4043	254	0.3818	4941	X-RAY DIFFRACTION	90.74
2.02-2.05	0.4412	215	0.4252	4438	X-RAY DIFFRACTION	82.32
2.05-2.07	0.4421	208	0.432	4582	X-RAY DIFFRACTION	84.24
2.07-2.1	0.3955	278	0.3601	4726	X-RAY DIFFRACTION	86.77
2.1-2.12	0.3463	284	0.289	5143	X-RAY DIFFRACTION	95.03
2.12-2.15	0.3097	227	0.2847	5128	X-RAY DIFFRACTION	93.49
2.15-2.18	0.316	234	0.2655	4508	X-RAY DIFFRACTION	83.87
2.18-2.22	0.2879	262	0.2643	5069	X-RAY DIFFRACTION	92.81
2.22-2.25	0.3652	224	0.3308	4879	X-RAY DIFFRACTION	90.53
2.25-2.29	0.2652	235	0.2626	5043	X-RAY DIFFRACTION	91.95
2.29-2.33	0.266	256	0.2199	5347	X-RAY DIFFRACTION	97.29
2.33-2.37	0.228	297	0.211	5368	X-RAY DIFFRACTION	97.35
2.37-2.42	0.2394	276	0.204	5165	X-RAY DIFFRACTION	96.59
2.42-2.46	0.2541	254	0.1981	5293	X-RAY DIFFRACTION	96.65
2.46-2.52	0.2456	291	0.1891	5308	X-RAY DIFFRACTION	97.53
2.52-2.58	0.2312	248	0.1954	5233	X-RAY DIFFRACTION	96.96
2.58-2.64	0.2441	291	0.2019	5247	X-RAY DIFFRACTION	96.72
2.64-2.71	0.2558	242	0.224	5220	X-RAY DIFFRACTION	94.88
2.71-2.79	0.2377	210	0.2052	5077	X-RAY DIFFRACTION	91.38
2.79-2.88	0.2406	271	0.1892	4919	X-RAY DIFFRACTION	92.17
2.88-2.99	0.1813	273	0.1863	5369	X-RAY DIFFRACTION	98.6
2.99-3.1	0.2674	257	0.1924	5484	X-RAY DIFFRACTION	98.54
3.11-3.25	0.2145	248	0.1798	5362	X-RAY DIFFRACTION	98.44
3.25-3.42	0.2374	233	0.1782	5408	X-RAY DIFFRACTION	97.97
3.42-3.63	0.1796	300	0.1631	5299	X-RAY DIFFRACTION	97.65
3.63-3.91	0.1519	242	0.142	5315	X-RAY DIFFRACTION	96.46
3.91-4.31	0.143	206	0.122	5067	X-RAY DIFFRACTION	91.21
4.31-4.93	0.16	333	0.1165	5369	X-RAY DIFFRACTION	98.99
4.93-6.21	0.1772	302	0.1463	5345	X-RAY DIFFRACTION	97.83
6.21-48.73	0.1715	301	0.1537	5284	X-RAY DIFFRACTION	94.23

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	3.10381924927	0.0406977069074	0.234061691231	1.3675878315	0.167304846179	1.15299370813	-0.114833030534	0.240165723258	0.0802117044971	-0.0741366180647	0.0765488039139	-0.455712552022	-0.146317551694	0.358724481794	0.0446035410064	0.259483609372	-0.0264840960331	-0.0221273346263	0.426803514472	-0.0323956198791	0.449244006637	46.8947772946	14.4116371587	31.7335721717
2	1.35554776966	0.635281437109	-0.319471010906	1.09256106695	-0.796560144009	1.10583848309	-0.0416475190455	0.028108925575	-0.337710204209	-0.0559135113733	0.0383628021658	-0.113798040869	0.10882558889	0.0863523203522	0.0322607649503	0.234237519123	0.0509092844989	-0.0267826636279	0.280042771184	-0.0965052725159	0.397775540951	21.818726396	-2.57234321179	36.7157184744
3	5.23568645835	3.21415197042	-1.54285198716	3.77296096963	-0.0391605303498	1.51311301679	-0.078968655116	-0.136155184397	-1.01883481775	-0.0273573256638	0.00622510739269	0.50812371159	0.430505052377	-0.503208166005	0.0837399203343	0.498428212723	-0.0424675022083	-0.11163903874	0.523952808996	0.143158747874	1.07567030733	-6.6986523456	-27.5424293623	50.5047362466
4	2.55858855023	0.441587848567	0.468857154368	1.62079289534	0.470358372833	1.84512378762	0.00336599477971	0.0811806953867	-0.510666113104	-0.0448787932738	0.0301527710468	0.23824049139	0.289716848462	-0.392507964968	-0.0296298439261	0.280240050778	-0.0432293329685	-0.0541304481314	0.384227026314	-0.0473971571431	0.466169130281	-14.8758679636	-8.10976130435	26.00863206
5	1.3352037535	0.725767699457	-0.165130791762	1.43766918785	-0.774752773521	1.02046526373	-0.117170116584	0.267253745776	-0.154039370392	-0.182279107329	0.10652803841	-0.00685507083103	0.040013449775	0.0507429232896	0.0152484240097	0.234119635683	0.00976063101963	-0.0216642812332	0.347374772957	-0.113937356758	0.287448451876	10.7361984251	7.68162033675	19.7086143853
6	5.1980443784	2.98464417834	-0.663847468072	3.79231063004	0.272702806136	1.70462058286	-0.441176349826	0.668066792631	0.22302434027	-0.395970078643	0.440396754066	-0.638408197394	-0.401495691912	0.786978344526	0.00184304375445	0.556687889877	-0.201109814165	-0.0233973409387	0.957919283491	0.0477066820761	0.513655713905	39.0338517193	32.6495912623	5.98036760053
7	2.47060741417	-0.733615738701	0.404120500175	1.63886749175	0.0758085877193	2.01539926686	-0.0972904767023	0.31634874537	0.362027770397	-0.227685224052	-0.0117966528411	0.211916055614	-0.418303790954	-0.307981935996	0.0815542626812	0.345556597297	0.0559063667717	-0.0983168871352	0.374368061506	0.0160190791635	0.412597923126	-12.5434523571	31.8290077359	21.2776167391
8	0.997509988965	0.243644672853	0.116022567405	1.32460445207	-0.963615450471	1.40908462101	-0.0635639336553	-0.206985145946	-0.0128081851615	0.112342856072	0.0695608900679	0.140032491697	-0.169642738386	-0.157586540999	-0.0252113982801	0.216984199263	0.0927028997394	-0.0157579954816	0.329973398084	-0.0770203654632	0.273054594177	-2.13051598677	16.0376590068	45.506140096
9	1.72073933867	-1.34148088877	1.03945641679	3.61174440363	-2.0466986378	4.56931029167	-0.218747660619	-1.06781109976	-0.577496877672	0.904320677706	0.386066135973	-0.0886208723109	0.00513113257855	-0.0326095893943	-0.144176838459	0.564817324413	0.103724030484	0.00194760428831	1.0166941805	0.205623543024	0.571138153245	3.98756263586	-9.06415908352	76.4988999777
10	2.1293034553	-0.178704475898	0.960529720439	1.6894479188	0.11541177993	2.93050162243	-0.0453114423157	-0.480244277433	-0.166345126971	0.444929381241	0.0862866563727	-0.259821021186	0.06052216512	0.0465565289208	-0.0314448639068	0.32892886639	0.0364803634128	-0.094068822077	0.407855090079	-0.00407566935364	0.349318304674	29.0842896105	9.35000736967	67.2491336246
11	0.991034716822	0.222122099931	0.101284303358	1.17922885461	-0.961332969697	1.5653826424	-0.13636200038	-0.0804877282086	0.174936641925	0.11084077379	0.0644899162057	-0.00671424310895	-0.254702588577	0.0147468303533	0.0688275246731	0.308605196159	0.0449339991621	-0.0752068030626	0.271837569646	-0.0961728327536	0.335086599488	18.1479530159	26.2460313925	44.1626330559
12	1.51017947818	-1.2180652806	1.33324746721	3.07598916346	-1.66840259444	4.78027456063	-0.275165138896	0.586066901261	0.475171854538	-0.380918678146	-0.00477651499431	0.332193140151	-0.960170215436	-0.0754977489892	0.300032166637	0.741556216352	-0.1100939524	-0.290526227679	0.534650448345	0.147233544089	0.812225904786	12.2861122262	51.1689363656	13.2554780694

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 1 through 157 )	A	A	1 - 157	1 - 157
2	2	chain 'A' and (resid 158 through 384 )	A	A	158 - 384	158 - 384
3	3	chain 'A' and (resid 385 through 461 )	A	A	385 - 461	385 - 461
4	4	chain 'B' and (resid 1 through 156 )	B	D	1 - 156	1 - 156
5	5	chain 'B' and (resid 157 through 384 )	B	D	157 - 384	157 - 384
6	6	chain 'B' and (resid 385 through 461 )	B	D	385 - 461	385 - 461
7	7	chain 'C' and (resid 1 through 156 )	C	G	1 - 156	1 - 156
8	8	chain 'C' and (resid 157 through 384 )	C	G	157 - 384	157 - 384
9	9	chain 'C' and (resid 385 through 461 )	C	G	385 - 461	385 - 461
10	10	chain 'D' and (resid 1 through 157 )	D	J	1 - 157	1 - 157
11	11	chain 'D' and (resid 158 through 384 )	D	J	158 - 384	158 - 384
12	12	chain 'D' and (resid 385 through 461 )	D	J	385 - 461	385 - 461

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

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 612 molecules

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Experimental details

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