PDB-3ztt: Crystal structure of pneumococcal surface antigen PsaA with manganese

ID or keywords:

Entry

Database: PDB / ID: 3ztt

Title

Crystal structure of pneumococcal surface antigen PsaA with manganese

Components

MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN

Keywords

METAL BINDING PROTEIN

Function / homology

Function and homology information

metal ion transport / cell adhesion / metal ion binding / plasma membrane
Similarity search - Function

Biological species

STREPTOCOCCUS PNEUMONIAE (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

McDevitt, C.A. / Ogunniyi, A.D. / Valkov, E. / Lawrence, M.C. / Kobe, B. / McEwan, A.G. / Paton, J.C.

Citation

Journal: PLoS Pathog. / Year: 2011
Title: A molecular mechanism for bacterial susceptibility to zinc.
Authors: McDevitt, C.A. / Ogunniyi, A.D. / Valkov, E. / Lawrence, M.C. / Kobe, B. / McEwan, A.G. / Paton, J.C.

History

Deposition	Jul 12, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 7, 2011	Provider: repository / Type: Initial release
Revision 1.1	Mar 28, 2018	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.2	Jun 20, 2018	Group: Advisory / Data collection / Derived calculations Category: pdbx_struct_conn_angle / pdbx_validate_symm_contact / struct_conn Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.dist
Revision 1.3	Feb 20, 2019	Group: Advisory / Data collection / Derived calculations Category: pdbx_data_processing_status / pdbx_validate_symm_contact ...pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ztt.cif.gz	446 KB	Display	PDBx/mmCIF format
PDB format	pdb3ztt.ent.gz	367.7 KB	Display	PDB format
PDBx/mmJSON format	3ztt.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3ztt_validation.pdf.gz	466.6 KB	Display	wwPDB validaton report
Full document	3ztt_full_validation.pdf.gz	511.5 KB	Display
Data in XML	3ztt_validation.xml.gz	46.6 KB	Display
Data in CIF	3ztt_validation.cif.gz	62.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zt/3ztt ftp://data.pdbj.org/pub/pdb/validation_reports/zt/3ztt	HTTPS FTP

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Related structure data

Related structure data	1pszS S: Starting model for refinement
Similar structure data	5kzj-1 6xpn-1 6xpn-2 4oxq-3 3gi1-2 5ax0-d 5afs-d 3hh8-d 5z2j-d 5uy4-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) 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

Related structure data

1pszS

S: Starting model for refinement

Similar structure data

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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: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN

B: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN

C: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN

D: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN

hetero molecules

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

1

A: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN

hetero molecules

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

2

B: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN

hetero molecules

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

3

C: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN

hetero molecules

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

4

D: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.334, 107.693, 77.942
Angle α, β, γ (deg.)	90.00, 95.67, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	1 - 310
2	1	1	2	B	1 - 310
3	1	1	2	C	1 - 310
4	1	1	2	D	1 - 310
1	1	2	2	B	1 - 310
2	1	2	2	A	1 - 310
3	1	2	2	C	1 - 310
4	1	2	2	D	1 - 310
1	1	3	2	C	1 - 310
2	1	3	2	A	1 - 310
3	1	3	2	B	1 - 310
4	1	3	2	D	1 - 310
1	1	4	4	D	1 - 310
2	1	4	4	A	1 - 310
3	1	4	4	B	1 - 310
4	1	4	4	C	1 - 310

NCS ensembles :

ID
1
2
3
4

#1: Protein	MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN / PNEUMOCOCCAL SURFACE ADHESIN A / PNEUMOCOCCAL SURFACE ANTIGEN A / PSAA Mass: 34143.254 Da / Num. of mol.: 4 / Fragment: RESIDUES 19-309 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0A4G3, UniProt: P0A4G2*PLUS
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.09 Å³/Da / Density % sol: 45.1 % / Description: NONE
Crystal grow	Details: 33% PEG 1500, 0.15 M SPG BUFFER PH 4.0, 0.2 M MNSO4.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.89445
Detector	Type: ADSC QUANTUM 315 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.89445 Å / Relative weight: 1
Reflection	Resolution: 2.74→19.8 Å / Num. obs: 28404 / % possible obs: 99.2 % / Observed criterion σ(I): 1.7 / Redundancy: 3.4 % / B_iso Wilson estimate: 75.1 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 9.3
Reflection shell	Resolution: 2.74→2.89 Å / R_merge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / % possible all: 73.1

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0066	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PSZ

1psz

Resolution: 2.7→19.73 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.917 / SU B: 29.345 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2464	1547	5.1 %	RANDOM
R_work	0.21507	-	-	-
obs	0.21668	29082	99.21 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 50.574 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.12 Å²	0 Å²	0.19 Å²
2-	-	-0.23 Å²	0 Å²
3-	-	-	0.15 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→19.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8867	0	4	153	9024

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	9039
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.627	1.972	12206
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.518	5	1108
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.924	26.857	420
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.527	15	1708
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	27.041	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	1340
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	6748
X-RAY DIFFRACTION	r_gen_planes_other
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	0.878	1.5	5547
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.778	2	8990
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.777	3	3492
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.982	4.5	3216
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1112	tight positional	0.03	0.05
1	2	B	1112	tight positional	0.03	0.05
1	3	C	1112	tight positional	0.03	0.05
1	4	D	1112	tight positional	0.03	0.05
2	2	A	1112	tight positional	0.03	0.05
2	1	B	1112	tight positional	0.03	0.05
2	3	C	1112	tight positional	0.03	0.05
2	4	D	1112	tight positional	0.03	0.05
3	2	A	1112	tight positional	0.03	0.05
3	3	B	1112	tight positional	0.03	0.05
3	1	C	1112	tight positional	0.03	0.05
3	4	D	1112	tight positional	0.03	0.05
1	1	A	1104	medium positional	0.03	0.5
1	2	B	1104	medium positional	0.03	0.5
1	3	C	1104	medium positional	0.03	0.5
1	4	D	1104	medium positional	0.03	0.5
2	2	A	1104	medium positional	0.03	0.5
2	1	B	1104	medium positional	0.03	0.5
2	3	C	1104	medium positional	0.03	0.5
2	4	D	1104	medium positional	0.03	0.5
3	2	A	1104	medium positional	0.03	0.5
3	3	B	1104	medium positional	0.03	0.5
3	1	C	1104	medium positional	0.03	0.5
3	4	D	1104	medium positional	0.03	0.5
4	2	A	2216	medium positional	0.03	0.5
4	3	B	2216	medium positional	0.03	0.5
4	4	C	2216	medium positional	0.03	0.5
4	1	D	2216	medium positional	0.03	0.5
1	1	A	1112	tight thermal	0.05	0.5
1	2	B	1112	tight thermal	0.05	0.5
1	3	C	1112	tight thermal	0.05	0.5
1	4	D	1112	tight thermal	0.05	0.5
2	2	A	1112	tight thermal	0.05	0.5
2	1	B	1112	tight thermal	0.05	0.5
2	3	C	1112	tight thermal	0.05	0.5
2	4	D	1112	tight thermal	0.05	0.5
3	2	A	1112	tight thermal	0.05	0.5
3	3	B	1112	tight thermal	0.05	0.5
3	1	C	1112	tight thermal	0.05	0.5
3	4	D	1112	tight thermal	0.05	0.5
1	1	A	1104	medium thermal	0.05	2
1	2	B	1104	medium thermal	0.05	2
1	3	C	1104	medium thermal	0.05	2
1	4	D	1104	medium thermal	0.05	2
2	2	A	1104	medium thermal	0.05	2
2	1	B	1104	medium thermal	0.05	2
2	3	C	1104	medium thermal	0.05	2
2	4	D	1104	medium thermal	0.05	2
3	2	A	1104	medium thermal	0.05	2
3	3	B	1104	medium thermal	0.05	2
3	1	C	1104	medium thermal	0.05	2
3	4	D	1104	medium thermal	0.05	2
4	2	A	2216	medium thermal	0.05	2
4	3	B	2216	medium thermal	0.05	2
4	4	C	2216	medium thermal	0.05	2
4	1	D	2216	medium thermal	0.05	2

LS refinement shell

Resolution: 2.7→2.769 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.604	112	-
R_work	0.509	2124	-
obs	-	-	99.38 %

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	0.8803	0.2897	1.0463	0.5423	0.0827	1.7801	-0.1248	-0.0395	0.118	-0.0721	0.0324	-0.0012	-0.1139	0.0316	0.0924	0.0372	-0.0014	-0.0115	0.0671	0.0075	0.0869	-31.5612	25.1878	-8.3197
2	0.5975	0.3043	0.53	1.0319	1.0114	1.9031	-0.026	0.0336	-0.0305	-0.2077	0.05	-0.1106	-0.1221	0.1074	-0.024	0.1114	-0.0034	0.0374	0.0888	0.02	0.0869	-47.499	-8.3019	-29.4575
3	0.66	-0.0568	0.3348	0.4352	0.3427	1.642	-0.0408	-0.001	-0.1074	-0.0697	0.054	0.0743	0.0085	-0.2061	-0.0132	0.0405	0.014	0.0147	0.1733	0.0411	0.0929	-62.1408	8.714	10.287
4	1.0901	0.5401	0.2442	1.8662	-0.591	1.7748	0.188	-0.2123	-0.0552	0.3998	-0.2195	-0.2051	-0.1448	0.2103	0.0316	0.0974	-0.0545	-0.0309	0.1499	0.0411	0.1081	-18.6707	5.3799	-44.6621

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	32 - 1000
2	X-RAY DIFFRACTION	2	B	32 - 1000
3	X-RAY DIFFRACTION	3	C	32 - 1000
4	X-RAY DIFFRACTION	4	D	32 - 1000

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