PDB-8fmd: Crystal Structure of Kemp Eliminase KE70-core in unbound state

ID or keywords:

Entry

Database: PDB / ID: 8fmd

Title

Crystal Structure of Kemp Eliminase KE70-core in unbound state

Components

Kemp Eliminase KE70-core

Keywords

LYASE / Artificial enzyme

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Zarifi, N. / Asthana, P. / Fraser, J.S. / Chica, R.A.

Funding support

Canada, 2items

Citation

Journal: To Be Published
Title: Crystal Structure of Kemp Eliminase KE70-core in unbound state
Authors: Zarifi, N. / Asthana, P. / Fraser, J.S. / Chica, R.A.

History

Deposition	Dec 23, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 10, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8fmd.cif.gz	340.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8fmd.ent.gz	231.5 KB	Display	PDB format
PDBx/mmJSON format	8fmd.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/fm/8fmd ftp://data.pdbj.org/pub/pdb/validation_reports/fm/8fmd	HTTPS FTP

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Related structure data

Related structure data	3nr0S S: Starting model for refinement

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Kemp Eliminase KE70-core

B: Kemp Eliminase KE70-core

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

1

A: Kemp Eliminase KE70-core

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

2

B: Kemp Eliminase KE70-core

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

Unit cell

Length a, b, c (Å)	62.915, 53.992, 81.455
Angle α, β, γ (deg.)	90.000, 110.872, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Kemp Eliminase KE70-core Mass: 28718.650 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3-Gold
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.127884 Å³/Da / Density % sol: 42.23202 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 25% w/v PEG6000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.11587 Å / Relative weight: 1
Reflection	Resolution: 2.2→76.11 Å / Num. obs: 26026 / % possible obs: 99.4 % / Redundancy: 6.39 % / B_iso Wilson estimate: 23.73 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.065 / R_pim(I) all: 0.028 / R_rim(I) all: 0.071 / Χ²: 1.06 / Net I/σ(I): 19
Reflection shell	Resolution: 2.2→2.27 Å / R_merge(I) obs: 0.146 / Mean I/σ(I) obs: 9.2 / Num. unique obs: 2178 / CC_1/2: 0.981 / R_pim(I) all: 0.07 / R_rim(I) all: 0.162 / Χ²: 0.79 / % possible all: 97.4

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
Coot	1.17.1_3660	model building
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3NR0

3nr0

Resolution: 2.2→76.11 Å / SU ML: 0.1949 / Cross valid method: FREE R-VALUE / σ(F): 2.06 / Phase error: 20.4284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1943	1260	4.84 %
R_work	0.1622	24751	-
obs	0.1638	26011	99.3 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.42 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→76.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3739	0	0	161	3900

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0021	3836
X-RAY DIFFRACTION	f_angle_d	0.52	5208
X-RAY DIFFRACTION	f_chiral_restr	0.0408	624
X-RAY DIFFRACTION	f_plane_restr	0.0035	675
X-RAY DIFFRACTION	f_dihedral_angle_d	12.844	1390

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 (%)
2.2-2.29	0.203	116	0.1748	2675	X-RAY DIFFRACTION	97.66
2.29-2.39	0.2208	125	0.172	2771	X-RAY DIFFRACTION	99.86
2.39-2.52	0.2237	138	0.1781	2759	X-RAY DIFFRACTION	99.66
2.52-2.68	0.2242	151	0.1786	2722	X-RAY DIFFRACTION	99.79
2.68-2.88	0.2421	126	0.182	2764	X-RAY DIFFRACTION	99.86
2.88-3.17	0.2226	123	0.1925	2788	X-RAY DIFFRACTION	99.66
3.17-3.63	0.2058	158	0.1741	2732	X-RAY DIFFRACTION	99.38
3.63-4.57	0.1552	169	0.1391	2707	X-RAY DIFFRACTION	98.66
4.58-76.11	0.1655	154	0.1297	2833	X-RAY DIFFRACTION	99.2

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	0.23649488936	-0.0435933364674	0.147896360476	0.344298748925	-0.0234551854985	0.184227931638	-0.178772472724	0.250847473212	0.492664023205	0.0365134307681	0.036065125305	-0.236189571892	-0.279851126167	0.0479207664325	-0.0212435832949	0.256330836763	0.0679801990101	-0.000141428076524	0.361494640445	0.0646058072374	0.31074533316	-2.04634558274	-4.07809962694	-8.7212319547
2	0.713107988252	-0.185854465883	0.311395837594	0.67443188603	-0.190654635198	0.986688220354	0.00986642169976	-0.0284048235743	0.0302512791547	0.00542985933092	-0.0648208400907	-0.0237932344567	0.0884474859515	0.13172503004	-0.00451852659414	0.136873103262	-0.00251550274357	0.00285557973957	0.145231732022	0.00344761866125	0.152239796655	-18.3335541431	-2.61059358405	-1.82419710294
3	0.250249878211	-0.085749305903	-0.0775017435849	0.134780019824	0.227182964915	0.406408542446	-0.0207593810564	-0.196756887474	0.180884753948	0.103547253043	0.0128427451746	-0.173207630026	0.0624317030509	0.129893421785	-0.00171322474249	0.125749610428	0.0276618561381	0.00177187925811	0.229355312242	0.0284158691432	0.231752626634	-3.45759666693	-5.36433567116	4.29060134154
4	0.0433756565024	-0.0233575566581	-0.0350178166001	0.0243696255685	0.0181733526736	0.0277718790578	0.0847427498774	0.348441188	0.250381959062	0.0390910441936	-0.117961266807	0.104458902118	-0.154127228942	-0.291270502075	-5.78787068603E-5	0.285385085211	0.0844655335602	0.015507455912	0.405654214527	0.0748694690225	0.299555543112	-39.5356354923	13.4546195379	-38.3355233275
5	0.0250537267978	0.0200184633627	-0.0139211506631	0.0240281500847	0.00813528369828	0.0520704436589	0.106364644391	-0.00407783829811	0.273643210906	-0.0520156726219	-0.0547745945726	-0.149521026879	-0.115024342894	0.113591018213	5.88771531941E-5	0.297267501725	-0.0127170909863	0.047602761963	0.2654068583	-0.0144322106785	0.315816518471	-25.0402157423	12.0511721415	-21.8383146474
6	0.142467004792	-0.0293805673204	-0.0996621982471	0.078089038202	-0.0385768477473	0.116531697512	-0.0130609682148	0.0100425957374	0.0964199290838	0.0850039372786	-0.00848995951605	-0.0275041825238	-0.109849711941	-0.17539809809	2.59853607997E-5	0.234465535108	0.0214243744879	0.00667236481592	0.203947298743	-0.0105990926794	0.225847339123	-33.85150584	8.21940215822	-21.8150782406
7	0.0819788451781	0.0951251948928	0.0943533189091	0.109896865856	0.108831976747	0.107497525374	0.0265077323282	0.0171186494142	-0.000719441787479	-0.0417761841134	-0.029994383058	-0.0943439400034	0.00525562247756	-0.0368761572125	4.16881898478E-6	0.218600243545	0.000917887716924	0.00338475275887	0.177146405829	0.00851664666651	0.214434253231	-28.4357370428	-0.20138917476	-26.7103546325
8	0.236309429681	-0.12566975529	0.231740533356	0.138833739635	-0.0154859598479	0.388672770362	-0.0861141588982	-0.0210974050564	-0.0481221080502	-0.00805451335071	0.0540423421842	0.00500689113617	0.170869849095	-0.139948719351	0.00663139603499	0.243077834344	0.00230398151111	0.00517069116747	0.121454674768	0.000495095597719	0.208341607764	-22.9094979022	-9.09001579331	-30.3366853857
9	0.0310691385206	-0.00356646325004	-0.0258037504957	0.000304459210155	0.00289610439347	0.0204811198729	0.0453622010696	0.179295773221	-0.222158833466	0.120297142732	-0.116034245597	-0.00730414164793	0.203744125113	-0.240101359684	0.00018253445515	0.26747143673	-0.0358886516199	0.0408257822382	0.201606854008	-0.0202479817444	0.231897027675	-28.5757408677	-15.5320422618	-31.0548006633
10	0.115309599843	-0.128772883865	-0.0135380588723	0.214508949102	0.0647182470892	0.0361554309003	0.0975035379648	0.0899787573306	0.300238294093	-0.0151485373361	0.0113909417473	0.0120364785747	0.118422679118	0.00765926814624	-0.000699616186428	0.219221676501	-0.000145898579326	0.00943518545338	0.215454231042	-0.00814208724978	0.177061622826	-25.3206965178	-4.5449470772	-38.2215667803
11	0.0283341746299	0.0159604816093	0.016820249406	0.0283014834854	0.00780485523445	0.0110977087566	0.0518932448049	0.21462941555	-0.129249882441	-0.0175984898996	-0.187560215759	-0.0568316583086	0.23423206784	-0.204962832177	0.000606734349072	0.303483093129	-0.0130042777703	-0.00911350905478	0.220654370958	-0.0300346302664	0.1901539632	-26.9829532878	-10.8340048881	-45.4766998438
12	0.00619630715322	0.00145925243117	-0.0149440103769	0.0111350439405	0.0405138844084	0.206342773083	0.13773325882	0.0379487121353	-0.0815651986355	-0.0958211051648	-0.106037029028	-0.0490221380789	0.0559713626823	-0.209132624236	-0.000441371214945	0.253902287502	-0.0010252748691	0.0346222090971	0.202523479271	0.00409510416159	0.223392369235	-25.5700033066	0.0979291006864	-38.7678044157
13	1.08536315986	-0.194788588453	-0.113266680143	0.23631986902	0.0924920808084	0.15225757141	0.0887273841307	0.673189089633	0.150563875123	-0.311518936237	0.0179544309909	-0.023596799404	-0.120044435435	-0.244304684552	0.00309879315982	0.293065364324	-0.0104310941436	-0.0138126426214	0.331277474581	-0.0177263777725	0.205878360939	-33.1494216749	-1.25705337494	-45.2438019949
14	0.0601954301259	-0.0886685833566	-0.0538800950586	0.193637793459	0.154770715214	0.135347491299	0.138044454774	0.372373273911	0.228635731917	-0.0978228074719	-0.0638885671491	0.0452548361608	-0.281916360675	-0.182815013319	-4.00742534083E-6	0.297455654643	0.0595167604149	0.0248385944381	0.427309272256	0.0644244155734	0.301210443148	-37.9647879756	5.61177280683	-43.6510954859
15	0.416699851765	0.5939912263	0.780087717832	0.87376476271	1.14348217458	1.49696804039	0.231035965384	0.217428806042	-0.0399290065581	-0.14782266593	-0.00708770746607	-0.391321404964	-0.23928685296	0.175041166244	0.18909096897	0.35560238955	0.114185136139	0.099435970918	0.297900887587	0.147853373331	0.389489746813	-34.8603529215	20.7164672141	-35.5891363958

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 193 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 194 through 252 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 18 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 19 through 36 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 37 through 63 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 64 through 83 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 84 through 116 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 117 through 133 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 134 through 148 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 149 through 162 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 163 through 179 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 180 through 209 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 210 through 239 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 240 through 253 )

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