PDB-6v3q: Crystal Structure of the Metallo-beta-Lactamase FIM-1 from Pseudo...

ID or keywords:

Entry

Database: PDB / ID: 6v3q

Title

Crystal Structure of the Metallo-beta-Lactamase FIM-1 from Pseudomonas aeruginosa in the Mono-Zinc Form

Components

Metallo-beta-lactamase FIM-1

Keywords

HYDROLASE / lactam antibiotics / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / ISOPROPYL ALCOHOL / Metallo-beta-lactamase FIM-1

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Kim, Y. / Hatzos-Skintges, C. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of the Metallo-beta-Lactamase FIM-1 from Pseudomonas aeruginosa in the Mono-Zinc Form
Authors: Kim, Y. / Hatzos-Skintges, C. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Nov 26, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2020	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6v3q.cif.gz	227.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6v3q.ent.gz	153.1 KB	Display	PDB format
PDBx/mmJSON format	6v3q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6v3q_validation.pdf.gz	442.5 KB	Display	wwPDB validaton report
Full document	6v3q_full_validation.pdf.gz	445.3 KB	Display
Data in XML	6v3q_validation.xml.gz	18.1 KB	Display
Data in CIF	6v3q_validation.cif.gz	24.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v3/6v3q ftp://data.pdbj.org/pub/pdb/validation_reports/v3/6v3q	HTTPS FTP

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Related structure data

Similar structure data	5eje-d 3fzy-d 3eeb-d 2nze-d 3fv5-d 4nwj-d 5xo6-1 6tbr-d 4qvs-1 4wd6-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP06560

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #105 - Sep 2008 Ribonuclease A similarity (2) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Metallo-beta-lactamase FIM-1

B: Metallo-beta-lactamase FIM-1

hetero molecules

50.1 kDa, 2 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)	128.109, 128.109, 41.420
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	145
Space group name H-M	P3₂
Space group name Hall	P3₂
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3

#1: Protein	Metallo-beta-lactamase FIM-1 Mass: 24930.014 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaFIM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: K7SA42
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 3.94 Å³/Da / Density % sol: 68.75 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M Sodium Citrate:HCl pH 5.6, 20% (v/v) 2-Propanol, 20% (w/v) PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 9, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. obs: 29670 / % possible obs: 99.4 % / Redundancy: 3.2 % / B_iso Wilson estimate: 60.8 Å² / R_merge(I) obs: 0.109 / Net I/σ(I): 15.7
Reflection shell	Resolution: 2.4→2.44 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.759 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 1495 / CC_1/2: 0.622

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: the undeposited structure of MBL from Hirschia baltica

Resolution: 2.4→41.93 Å / SU ML: 0.3067 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.9862

	R_factor	Num. reflection	% reflection
R_free	0.1848	1557	5.25 %
R_work	0.1646	-	-
obs	0.1657	29638	99.28 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 71.29 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→41.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3454	0	6	52	3512

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0024	3587
X-RAY DIFFRACTION	f_angle_d	0.5697	4903
X-RAY DIFFRACTION	f_chiral_restr	0.0467	548
X-RAY DIFFRACTION	f_plane_restr	0.0036	642
X-RAY DIFFRACTION	f_dihedral_angle_d	16.3558	2118

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 (%)
2.4-2.47	0.3084	135	0.2856	2527	X-RAY DIFFRACTION	97.76
2.47-2.56	0.2785	170	0.2704	2541	X-RAY DIFFRACTION	99.52
2.56-2.67	0.2721	176	0.2605	2518	X-RAY DIFFRACTION	99.41
2.67-2.79	0.2707	122	0.2485	2590	X-RAY DIFFRACTION	99.38
2.79-2.93	0.2949	140	0.2272	2572	X-RAY DIFFRACTION	99.74
2.93-3.12	0.2604	118	0.2136	2578	X-RAY DIFFRACTION	99.74
3.12-3.36	0.2076	162	0.1911	2523	X-RAY DIFFRACTION	99.78
3.36-3.7	0.1752	110	0.1692	2579	X-RAY DIFFRACTION	99.45
3.7-4.23	0.1513	105	0.1444	2603	X-RAY DIFFRACTION	99.49
4.23-5.33	0.1507	185	0.122	2502	X-RAY DIFFRACTION	99.44
5.33-41.93	0.1529	134	0.1299	2548	X-RAY DIFFRACTION	98.57

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	1.14509673019	-1.65470176932	2.10906165665	6.93262910079	0.000513828881164	5.93470415476	-0.802221803425	1.72219062946	-0.179452066232	-1.06135179317	1.02574955149	0.593209817466	0.167943403345	-0.535796711296	-0.229263565846	0.566132604043	-0.0650839444773	-0.0866212551368	0.807411408079	0.00432554495614	0.535276326163	41.4496554363	16.8250241129	-11.2028473966
2	3.24390366544	0.68315226334	-2.21596419161	2.05512569377	-0.434651471535	2.6483517007	0.0522724040234	0.308701305022	-0.599713249556	0.238600076829	0.0419871957376	0.280073326625	-0.0595222204476	-0.559818082982	-0.0574653560405	0.603455606705	-0.108286980034	-0.0841279584669	0.783508714243	0.0482650070144	0.720464197961	38.1940484209	15.2596086152	-3.48009717769
3	1.97545320851	-0.489676585576	0.243395413523	3.80293227096	1.31312734162	5.15887071147	-0.158678041864	0.446762116315	-0.391918207539	-0.320288102459	0.14327871145	0.101406767309	0.593140885131	-0.050402376644	0.0554570516183	0.586488806757	-0.131895506488	0.0297901867349	0.598738391568	-0.0222378467029	0.464102111522	50.359787461	13.1723817781	-8.33116075986
4	4.19520523564	0.735215445893	2.8528566681	4.46783031875	-0.286984833998	4.93354541102	0.274701378994	0.150464030436	-0.591144162201	0.100594004708	-0.283376697266	-0.225628549742	0.899979218218	-0.136103148338	0.0374578228548	0.656147641358	-0.0662073806613	0.050222021883	0.623905310538	-0.0528219160037	0.621147476135	55.2872265099	10.6541457502	-3.09862186254
5	4.23173825184	4.17136773265	-1.46283409768	4.22443532334	-1.78423362701	7.55935736081	0.244030637815	-1.11839685209	-0.442869394935	1.34646872563	-0.753653685305	-0.070107960935	0.61526928849	-0.002315229019	0.515532064094	1.06065691095	-0.0534664154134	-0.0328073362107	0.732864234869	0.0622012755301	0.728223939115	56.6892020147	9.54032615145	9.65954256252
6	5.10458931082	-2.87594299542	-1.47786649923	4.13467573846	3.2961363322	9.68389592517	0.045365343609	-0.481090482757	-0.23834739738	0.405835312709	-0.0493360500613	-0.349303804646	-0.321555245622	0.99595332304	-0.0667586255957	0.575245055668	-0.0719408188358	-0.0400643774089	0.54922325665	0.0603842504457	0.519836255863	61.1299994128	22.8089207516	5.95772741831
7	3.58553944537	-1.84106233658	-0.283455783104	4.14450635011	2.7709583582	5.84193048142	0.0143603985498	0.00422383190162	0.0253497191703	0.268102200575	-0.0764924079469	0.226640505023	0.245883645062	-0.342173722137	0.0936583478633	0.448256227917	-0.0950146360208	-0.00470373221738	0.479615891028	0.0272867814202	0.50164865811	49.4954191657	30.4901773986	5.49044469316
8	1.62227555679	-1.42367286956	-2.40444389063	6.25089500394	-0.331612528636	5.10663039763	-0.853598695009	1.50529735703	-0.259941710031	-0.936207135311	1.08494801876	-0.733747881577	-0.373394294418	0.73539841348	-0.18737079921	0.639096008651	-0.0994040005705	0.0285891313157	0.880334868049	-0.0102817219285	0.632422070046	22.5953765958	20.1686975925	-11.2308134252
9	3.49926632706	1.80317644945	2.49326679069	2.58352403707	0.895999766524	2.33518035401	0.258109905701	0.310154581736	0.562721347753	0.331620724519	-0.0885002911069	-0.255755433507	0.0903455106332	0.518073574561	0.0171316833669	0.597433705379	-0.146768537842	0.0936886179814	0.798432177	-0.0787918755316	0.727569234559	25.8539213853	21.7373299242	-3.47096930512
10	7.88523214534	-0.109712802199	0.299127085584	4.56073389279	-1.02271034059	5.22767762629	-0.0168500804429	0.832901172526	0.377052490544	-0.339471535744	0.163829117138	0.074066127209	-0.358075055362	0.140402343577	0.0241427943529	0.572848385023	-0.0865904838415	0.0100553133171	0.546778399565	0.032778175811	0.424226554523	12.7599712572	20.9764794681	-6.58990538897
11	7.95543799547	0.814830850041	0.395460545012	7.44505171023	0.406633603388	8.30402734678	-0.683690000348	0.576008436843	0.870596731795	-0.854171327804	0.118348317064	0.0436763667946	-1.40731554964	0.0163535048937	0.0704372038201	0.786616325141	-0.167438742279	-0.0623044664791	0.692770767598	0.0702468257207	0.635697584257	15.1637038169	28.4859154788	-11.1877210635
12	3.89536289257	0.341042689801	-1.84418731335	5.20536120231	0.28956494124	7.03622619456	0.0249282931577	0.149709723126	0.442145626357	0.135861160541	-0.157029607671	0.0756571075037	-1.08314367741	0.36825175697	0.252508338573	0.599831095269	-0.0893476585028	-0.0384904540359	0.600304868495	0.0667923357758	0.600496403812	8.77789691046	26.3010535638	-3.09544755434
13	6.6460386899	2.14105513221	-0.441313873443	6.94768693672	0.101254930649	7.88676585286	0.16966260792	-1.70953752648	0.700264575822	0.925663899601	-0.859231374193	-0.432944996557	-1.11543402964	-0.206943976417	0.176411405697	0.934385566738	-0.054876530238	0.00712574969634	0.731707237195	-0.0927389883098	0.697736614653	7.26887434054	27.5884132159	9.51220569283
14	8.00293426264	-1.87008469066	1.73974485104	3.56947799931	-2.54994440962	6.55843179394	0.0829881607724	-0.473236245855	0.214660711674	0.496221827333	-0.0157640270374	0.375600307817	0.331179900731	-0.883982288881	0.0214118373856	0.577198978661	-0.0480790846966	0.0401468855021	0.558557779351	-0.0604880270552	0.508972926241	2.9442340121	14.1515731177	5.95253306396
15	3.30898287798	-1.67286815976	-0.698627770868	3.89933756999	-3.23251013613	6.65661309289	-0.0238792289248	0.105465514615	-0.131793233542	0.202187903411	-0.0558865313891	-0.229847982128	-0.215306751758	0.339633713725	0.0917912546619	0.46899327712	-0.0978616467009	0.00240372489239	0.446531923465	-0.0384040647049	0.519126078285	14.5580808809	6.48777598867	5.47933741813

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 15 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 29 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 30 through 65 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 66 through 100 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 101 through 120 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 121 through 147 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 148 through 225 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 0 through 15 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 16 through 29 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 30 through 52 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 53 through 65 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 66 through 100 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 101 through 120 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 121 through 147 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 148 through 225 )

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