PDB-2p99: E. coli methionine aminopeptidase monometalated with inhibitor YE6

ID or keywords:

Entry

Database: PDB / ID: 2p99

Title

E. coli methionine aminopeptidase monometalated with inhibitor YE6

Components

Methionine aminopeptidase

Keywords

HYDROLASE / monometalated / mononuclear / Mn(II)-form / enzyme-inhibitor complex / metalloenzyme

Function / homology

Function and homology information

methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / ferrous iron binding / proteolysis / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Ye, Q.

Citation

Journal: J.Med.Chem. / Year: 2007
Title: Inhibition of Monometalated Methionine Aminopeptidase: Inhibitor Discovery and Crystallographic Analysis.
Authors: Huang, M. / Xie, S.X. / Ma, Z.Q. / Huang, Q.Q. / Nan, F.J. / Ye, Q.Z.

History

Deposition	Mar 24, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 20, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2p99.cif.gz	69 KB	Display	PDBx/mmCIF format
PDB format	pdb2p99.ent.gz	48.9 KB	Display	PDB format
PDBx/mmJSON format	2p99.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2p99_validation.pdf.gz	437.8 KB	Display	wwPDB validaton report
Full document	2p99_full_validation.pdf.gz	442.9 KB	Display
Data in XML	2p99_validation.xml.gz	14.1 KB	Display
Data in CIF	2p99_validation.cif.gz	19.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p9/2p99 ftp://data.pdbj.org/pub/pdb/validation_reports/p9/2p99	HTTPS FTP

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Related structure data

Related structure data	2p98C 2p9aC 2gtx C: citing same article (ref.)
Similar structure data	4z7m-1 1c22-d 2q94-d 4z7m-2 2evm-d 3d27-d 2p98-d 1xnz-d 2q92-d 1zbu-1 1c27-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

Deposited unit

A: Methionine aminopeptidase

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	38.310, 61.700, 50.640
Angle α, β, γ (deg.)	90.00, 105.43, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Methionine aminopeptidase / MAP / Peptidase M Mass: 28995.443 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: map / Plasmid: pGEMEX-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AE18, methionyl aminopeptidase
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-YE6 / 5-(2-chlorophenyl)furan-2-carbohydrazide Mass: 236.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₉ClN₂O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 152 / 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: 1.99 Å³/Da / Density % sol: 38.16 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG 20000, 0.1 M MES (pH 6.5), vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction

ID	Crystal-ID
1	1
2	1

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å

Detector

Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.8→20 Å / Num. obs: 20706 / % possible obs: 97.9 % / Redundancy: 3.7 % / R_merge(I) obs: 0.051 / R_sym value: 0.051 / Net I/σ(I): 10.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.8-1.9	3.7	0.337	2.2	10812	2952	0.337	95.9
1.9-2.01	3.7	0.213	3.4	10467	2835	0.213	96.8
2.01-2.15	3.7	0.146	4.9	9658	2620	0.146	97.1
2.15-2.32	3.7	0.103	7	9154	2473	0.103	97.8
2.32-2.55	3.7	0.072	9.8	8654	2336	0.072	98.6
2.55-2.85	3.7	0.052	13.4	7822	2103	0.052	98.9
2.85-3.29	3.7	0.043	15.2	6949	1862	0.043	99.6
3.29-4.02	3.7	0.033	18.1	5942	1589	0.033	99.8
4.02-5.69	3.7	0.028	20.9	4664	1255	0.028	100
5.69-19.14	3.6	0.034	15.3	2462	681	0.034	97.7

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Phasing

Phasing MR

R_factor: 0.357 / Cor.coef. F_o:F_c: 0.679

	Highest resolution	Lowest resolution
Rotation	3 Å	19.14 Å
Translation	3 Å	19.14 Å

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Processing

Software

Name	Version	Classification
SCALA		data scaling
MOLREP		phasing
CNS		refinement
PDB_EXTRACT	2	data extraction
MOSFLM		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / FOM work R set: 0.818 / σ(F): 0

	R_factor	Num. reflection	% reflection
R_free	0.263	2038	9.6 %
R_work	0.227	-	-
obs	-	20689	97.7 %

Solvent computation

B_sol: 35.936 Å²

Displacement parameters

B_iso mean: 26.323 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.537 Å²	0 Å²	3.522 Å²
2-	-	-3.201 Å²	0 Å²
3-	-	-	1.664 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2027	0	18	152	2197

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	c_bond_d	0.006
X-RAY DIFFRACTION	c_angle_d	1.359
X-RAY DIFFRACTION	c_mcbond_it	1.341	1.5
X-RAY DIFFRACTION	c_scbond_it	2	2
X-RAY DIFFRACTION	c_mcangle_it	2.016	2
X-RAY DIFFRACTION	c_scangle_it	2.909	2.5

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 40

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs
1.8-1.82	0.515	43	0.433	494	537
1.82-1.83	0.421	46	0.36	423	469
1.83-1.85	0.333	46	0.333	456	502
1.85-1.86	0.309	62	0.342	445	507
1.86-1.88	0.375	47	0.314	459	506
1.88-1.9	0.348	43	0.328	466	509
1.9-1.92	0.326	57	0.312	448	505
1.92-1.94	0.317	44	0.28	460	504
1.94-1.96	0.297	50	0.267	467	517
1.96-1.98	0.37	38	0.29	444	482
1.98-2	0.343	51	0.289	476	527
2-2.03	0.304	41	0.268	465	506
2.03-2.05	0.282	55	0.271	451	506
2.05-2.08	0.336	44	0.239	452	496
2.08-2.1	0.241	48	0.23	485	533
2.1-2.13	0.279	48	0.241	462	510
2.13-2.16	0.281	47	0.247	448	495
2.16-2.2	0.33	50	0.261	479	529
2.2-2.23	0.314	61	0.241	445	506
2.23-2.27	0.322	45	0.254	466	511
2.27-2.31	0.327	59	0.266	459	518
2.31-2.35	0.272	49	0.237	477	526
2.35-2.39	0.293	58	0.235	464	522
2.39-2.44	0.317	41	0.242	456	497
2.44-2.5	0.248	48	0.237	480	528
2.5-2.55	0.223	40	0.221	484	524
2.55-2.62	0.265	56	0.24	455	511
2.62-2.69	0.23	54	0.218	468	522
2.69-2.77	0.253	46	0.235	477	523
2.77-2.86	0.31	58	0.239	464	522
2.86-2.96	0.277	70	0.218	477	547
2.96-3.07	0.261	47	0.236	463	510
3.07-3.21	0.26	50	0.231	485	535
3.21-3.38	0.249	63	0.219	456	519
3.38-3.59	0.249	62	0.211	475	537
3.59-3.87	0.204	51	0.198	478	529
3.87-4.26	0.233	58	0.17	474	532
4.26-4.86	0.184	55	0.165	479	534
4.86-6.1	0.26	57	0.199	486	543
6.1-20	0.2	50	0.179	503	553

Xplor file

Refine-ID	Serial no	Param file	Topol file
X-RAY DIFFRACTION	1	CNS_TOPPAR:protein_rep.param	CNS_TOPPAR:protein_1.top
X-RAY DIFFRACTION	2	CNS_TOPPAR:dna-rna_rep.param	CNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION	3	CNS_TOPPAR:water_rep.param	CNS_TOPPAR:water.top
X-RAY DIFFRACTION	4	CNS_TOPPAR:ion.param	CNS_TOPPAR:ion.top
X-RAY DIFFRACTION	5	YE6.param	YE6.top

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