PDB-5kzt: Listeria monocytogenes OppA bound to peptide

ID or keywords:

Entry

Database: PDB / ID: 5kzt

Title

Listeria monocytogenes OppA bound to peptide

Components

Hexamer peptide: SER-ASP-GLU-SER-LYS-GLY
Hexamer peptide: SER-ASP-GLU-SER-SER-GLY
Peptide/nickel transport system substrate-binding protein

Keywords

PEPTIDE BINDING PROTEIN / substrate binding protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

peptide transport / peptide transmembrane transporter activity / cell envelope / ATP-binding cassette (ABC) transporter complex / periplasmic space
Similarity search - Function

Biological species

Listeria monocytogenes serotype 1/2a

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Light, S.H. / Whiteley, A.T. / Minasov, G. / Portnoy, D.A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Listeria monocytogenes OppA bound to peptide
Authors: Light, S.H. / Whiteley, A.T. / Minasov, G. / Portnoy, D.A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases

History

Deposition	Jul 25, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 10, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5kzt.cif.gz	429.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5kzt.ent.gz	351.2 KB	Display	PDB format
PDBx/mmJSON format	5kzt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kz/5kzt ftp://data.pdbj.org/pub/pdb/validation_reports/kz/5kzt	HTTPS FTP

-
Related structure data

Related structure data	4fajS S: Starting model for refinement
Similar structure data	1jet-d 3tcf-7 1b2h-d 1b3h-d 1b46-d 3o9p-d 1b4z-d 1b51-d 1b52-d 4faj-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Peptide/nickel transport system substrate-binding protein

B: Peptide/nickel transport system substrate-binding protein

C: Hexamer peptide: SER-ASP-GLU-SER-LYS-GLY

D: Hexamer peptide: SER-ASP-GLU-SER-SER-GLY

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

1

A: Peptide/nickel transport system substrate-binding protein

C: Hexamer peptide: SER-ASP-GLU-SER-LYS-GLY

defined by author&software
61.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Peptide/nickel transport system substrate-binding protein

D: Hexamer peptide: SER-ASP-GLU-SER-SER-GLY

defined by author&software
61.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	100.277, 74.630, 155.061
Angle α, β, γ (deg.)	90.00, 109.38, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Peptide/nickel transport system substrate-binding protein Mass: 60697.156 Da / Num. of mol.: 2 / Fragment: UNP residues 32-558 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serotype 1/2a (strain 10403S) (bacteria) Strain: 10403S / Gene: LMRG_01636 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3GJB6
#2: Protein/peptide	Hexamer peptide: SER-ASP-GLU-SER-LYS-GLY Mass: 622.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: Protein/peptide	Hexamer peptide: SER-ASP-GLU-SER-SER-GLY Mass: 580.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1113 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.9 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop Details: Protein solution: 12.0 mg/ml, 0.01 M Tris-HCl pH 8.3, and 10/mg/ml tryptone Crystallization condition: Classics II (Qiagen) D10: 0.1 M Bis-Tris pH 6.5 and 20% (w/v) PEG 5000 MME

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 1.85→30 Å / Num. obs: 92580 / % possible obs: 98.4 % / Redundancy: 3.2 % / R_merge(I) obs: 0.108 / Net I/σ(I): 17.3
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 3 % / R_merge(I) obs: 0.618 / Mean I/σ(I) obs: 2.3 / CC_1/2: 0.58 / % possible all: 99.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4FAJ

4faj

Resolution: 1.85→30 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.94 / SU B: 5.714 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20489	4604	5 %	RANDOM
R_work	0.16726	-	-	-
obs	0.16914	87975	97.04 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 21.565 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.42 Å²	-0 Å²	-0.07 Å²
2-	-	0.08 Å²	0 Å²
3-	-	-	0.31 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8236	0	0	1113	9349

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.02	8446
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	7891
X-RAY DIFFRACTION	r_angle_refined_deg	1.321	1.955	11444
X-RAY DIFFRACTION	r_angle_other_deg	0.892	3	18254
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.907	5	1037
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.719	26.256	422
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.337	15	1499
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.962	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	1245
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	9711
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1875
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.551	1.38	4148
X-RAY DIFFRACTION	r_mcbond_other	0.55	1.379	4147
X-RAY DIFFRACTION	r_mcangle_it	0.932	2.062	5185
X-RAY DIFFRACTION	r_mcangle_other	0.932	2.063	5186
X-RAY DIFFRACTION	r_scbond_it	0.723	1.46	4298
X-RAY DIFFRACTION	r_scbond_other	0.723	1.46	4299
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.199	2.148	6260
X-RAY DIFFRACTION	r_long_range_B_refined	5.258	12.562	10795
X-RAY DIFFRACTION	r_long_range_B_other	5.258	12.559	10794
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.85→1.877 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.261	262	-
R_work	0.238	5462	-
obs	-	-	81.62 %

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	1.8989	0.501	-0.1255	0.6986	-0.0227	0.5855	0.0062	0.0251	-0.2359	0.0159	-0.0095	-0.06	0.0315	-0.0441	0.0034	0.0292	-0.0008	0.0061	0.0247	-0.0164	0.0422	33.1962	10.977	20.3984
2	1.7777	0.7609	-0.5534	1.0631	-0.5781	0.9808	0.0613	-0.1318	-0.2365	0.0651	-0.0954	-0.1943	-0.0466	0.1087	0.0341	0.0227	0.0081	-0.0005	0.0624	-0.0138	0.1069	55.3781	18.2288	20.8156
3	1.2132	0.0323	-0.1474	1.072	0.5552	1.156	0.0732	0.1164	0.3222	-0.0427	-0.0091	-0.0159	-0.1169	-0.0341	-0.0641	0.046	0.0268	0.0595	0.0231	0.0545	0.1337	35.8402	44.964	16.2625
4	2.5635	-1.439	-0.2952	4.5471	0.0185	1.4207	0.0776	-0.1367	0.4965	0.0501	0.065	-0.3251	-0.0824	0.0779	-0.1426	0.0406	-0.0301	0.0535	0.027	-0.0616	0.1817	46.0565	48.3175	26.8271
5	1.5569	0.0437	-0.145	1.3782	0.4709	1.1227	0.0312	0.0032	0.0899	0.0828	0.0255	0.0019	-0.0392	-0.0216	-0.0568	0.033	0.016	0.023	0.0156	0.0114	0.0216	33.0569	33.2122	23.6132
6	3.4111	0.2909	2.5166	5.1388	2.5951	7.2048	0.066	0.0568	-0.0584	0.1791	-0.1418	0.644	0.2003	-0.6417	0.0758	0.0137	-0.0025	0.0251	0.1868	0.0343	0.1031	21.715	32.1431	7.522
7	3.0868	-1.2191	-0.5563	1.2882	0.3463	0.249	0.1135	0.144	0.0905	-0.114	-0.0433	-0.0544	-0.0836	-0.0029	-0.0701	0.0511	0.016	0.0333	0.0726	0.024	0.0375	44.6678	32.8225	12.6863
8	6.2286	-2.1345	-1.0101	2.6625	0.3922	0.6451	0.0128	0.1975	0.0287	-0.0771	-0.0225	-0.2205	0.019	-0.0057	0.0097	0.0158	-0.0013	0.0214	0.0362	-0.0314	0.0637	51.9598	15.587	11.3066
9	1.1267	-0.3187	0.0124	1.0459	-0.0213	0.5466	0.0364	0.0191	0.0552	-0.0622	-0.0514	0.0701	-0.0515	-0.0468	0.015	0.0535	0.0174	-0.0008	0.0207	0.0034	0.0168	7.6239	35.7413	52.4191
10	1.0638	-0.7052	0.4577	1.3057	-0.6011	1.0987	0.0951	0.1357	0.1141	-0.1034	-0.1185	-0.153	0.0397	0.0752	0.0234	0.0228	-0.0034	0.0196	0.0425	0.0143	0.0448	29.5935	28.3176	51.9908
11	0.4654	-0.0419	0.1071	1.0957	0.5988	0.8657	0.0082	-0.0392	-0.0807	0.0415	-0.0335	0.0387	0.0652	-0.043	0.0253	0.0332	-0.0076	-0.003	0.0144	0.0102	0.0198	9.9243	1.7754	57.3294
12	2.1264	1.2608	0.4079	4.2086	-0.1603	1.3704	0.0039	0.1103	-0.1943	-0.0874	0.0242	-0.2458	0.0462	0.0911	-0.0281	0.0252	0.0148	0.002	0.0353	-0.0221	0.0312	20.1064	-1.8957	46.9083
13	0.7921	-0.1102	0.1264	1.039	0.1129	0.4026	-0.0017	0.0531	0.042	-0.0821	0.0111	0.0322	0.0075	-0.0141	-0.0094	0.0331	-0.0131	-0.0075	0.0105	0.0072	0.0068	8.9431	13.6731	48.9811
14	7.7036	-1.4204	2.7858	3.6931	-1.4207	3.1909	-0.1755	-0.1813	-0.1035	-0.0842	0.1891	0.117	-0.0481	-0.3203	-0.0137	0.0172	0.0121	-0.0067	0.0535	0.0052	0.0361	-7.3257	12.1773	56.0835
15	9.0478	-1.7593	-3.4359	7.5815	3.0211	9.617	0.031	0.1849	0.4574	-0.0992	0.1237	0.4406	-0.1442	-0.4363	-0.1548	0.003	0.0071	-0.0037	0.0584	0.0238	0.0661	-4.1222	16.8017	68.2376
16	0.3679	0.2139	0.1239	0.9847	0.0038	0.1956	0.0323	-0.0294	0.0262	0.0667	-0.0391	-0.0447	0.0248	0.0106	0.0067	0.0351	-0.0006	0.0014	0.0391	0.0048	0.0144	20.3494	20.1638	61.1663

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	42 - 208
2	X-RAY DIFFRACTION	2	A	209 - 298
3	X-RAY DIFFRACTION	3	A	299 - 394
4	X-RAY DIFFRACTION	4	A	395 - 432
5	X-RAY DIFFRACTION	5	A	433 - 487
6	X-RAY DIFFRACTION	6	A	488 - 511
7	X-RAY DIFFRACTION	7	A	512 - 540
8	X-RAY DIFFRACTION	8	A	541 - 559
9	X-RAY DIFFRACTION	9	B	41 - 208
10	X-RAY DIFFRACTION	10	B	209 - 298
11	X-RAY DIFFRACTION	11	B	299 - 394
12	X-RAY DIFFRACTION	12	B	395 - 432
13	X-RAY DIFFRACTION	13	B	433 - 482
14	X-RAY DIFFRACTION	14	B	483 - 490
15	X-RAY DIFFRACTION	15	B	500 - 508
16	X-RAY DIFFRACTION	16	B	509 - 559

-
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