PDB-7uc3: Intramolecular ester bond-containing repeat domain from G. berger...

ID or keywords:

Entry

Database: PDB / ID: 7uc3

Title

Intramolecular ester bond-containing repeat domain from G. bergeri adhesin

Components

Adhesin

Keywords

CELL ADHESION / Repeat domain / adhesin / intramolecular ester bond / Ig-like fold

Function / homology

Pilus-presented adhesin helical insertion domain / T-Q ester bond containing domain / T-Q ester bond containing domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold / metal ion binding / membrane / Putative Cna protein B-type domain protein

Function and homology information

Biological species

Gemella bergeri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.442 Å

Authors

Wardega, J.K. / Squire, C.J. / Young, P.G.

Funding support

1items

Citation

Journal: To Be Published
Title: Intramolecular ester bond-containing repeat domain from G. bergeri adhesin
Authors: Wardega, J.K. / Squire, C.J. / Young, P.G.

History

Deposition	Mar 15, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 22, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7uc3.cif.gz	73.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7uc3.ent.gz		Display	PDB format
PDBx/mmJSON format	7uc3.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/uc/7uc3 ftp://data.pdbj.org/pub/pdb/validation_reports/uc/7uc3	HTTPS FTP

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Related structure data

Related structure data	4ni6S S: Starting model for refinement
Similar structure data	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: Adhesin

hetero molecules

17.1 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)	31.542, 46.647, 48.536
Angle α, β, γ (deg.)	90.000, 90.594, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Adhesin Mass: 17036.812 Da / Num. of mol.: 1 / Fragment: Repeat domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gemella bergeri (bacteria) / Gene: HMPREF1983_01328 / Plasmid: pProEXHta / Production host: Escherichia coli (E. coli) / References: UniProt: U2Q1B9
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	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: 2.1 Å³/Da / Density % sol: 41.31 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2 M NaCl, 0.1 M Bis-Tris Cl, and 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9778 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9778 Å / Relative weight: 1
Reflection	Resolution: 1.442→48.533 Å / Num. obs: 24975 / % possible obs: 96.8 % / Redundancy: 26.5 % / CC_1/2: 1 / R_merge(I) obs: 0.067 / R_pim(I) all: 0.013 / R_rim(I) all: 0.068 / Χ²: 0.52 / Net I/σ(I): 22
Reflection shell	Resolution: 1.45→1.48 Å / Redundancy: 16.7 % / Num. unique obs: 713 / CC_1/2: 0.479 / R_pim(I) all: 0.354 / % possible all: 58.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ni6

4ni6

Resolution: 1.442→48.533 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.943 / SU B: 3.055 / SU ML: 0.053 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2226	1229	4.921 %	Random selection
R_work	0.1679	23746	-	-
all	0.171	-	-	-
obs	-	24975	97.788 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 20.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.569 Å²	-0 Å²	-2.71 Å²
2-	-	2.654 Å²	0 Å²
3-	-	-	-3.166 Å²

Refinement step

Cycle: LAST / Resolution: 1.442→48.533 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1101	0	1	153	1255

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	1123
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1033
X-RAY DIFFRACTION	r_angle_refined_deg	1.272	1.646	1524
X-RAY DIFFRACTION	r_angle_other_deg	1.288	1.596	2406
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.277	5	146
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.855	27.551	49
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.535	15	195
X-RAY DIFFRACTION	r_chiral_restr	0.05	0.2	151
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1280
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	208
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	182
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.17	0.2	1015
X-RAY DIFFRACTION	r_nbtor_refined	0.151	0.2	534
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.071	0.2	542
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.115	0.2	111
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.122	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.198	0.2	34
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.14	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	1.355	1.91	581
X-RAY DIFFRACTION	r_mcbond_other	1.337	1.905	580
X-RAY DIFFRACTION	r_mcangle_it	1.875	2.874	725
X-RAY DIFFRACTION	r_mcangle_other	1.883	2.878	726
X-RAY DIFFRACTION	r_scbond_it	1.591	2.154	542
X-RAY DIFFRACTION	r_scbond_other	1.59	2.16	543
X-RAY DIFFRACTION	r_scangle_it	1.936	3.101	798
X-RAY DIFFRACTION	r_scangle_other	1.935	3.107	799
X-RAY DIFFRACTION	r_lrange_it	3.312	23.758	1212
X-RAY DIFFRACTION	r_lrange_other	3.156	23.445	1196
X-RAY DIFFRACTION	r_rigid_bond_restr	0.839	3	2156

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.442-1.479	0.312	83	0.262	1554	0.265	1873	0.797	0.844	87.3999	0.202
1.479-1.519	0.246	83	0.19	1690	0.193	1826	0.895	0.913	97.0975	0.155
1.519-1.563	0.229	82	0.168	1673	0.17	1796	0.911	0.937	97.7171	0.131
1.563-1.612	0.214	107	0.156	1577	0.16	1720	0.942	0.946	97.907	0.123
1.612-1.664	0.213	80	0.138	1566	0.142	1683	0.941	0.955	97.8015	0.114
1.664-1.723	0.274	62	0.129	1516	0.134	1602	0.926	0.957	98.5019	0.111
1.723-1.788	0.208	61	0.177	1462	0.178	1551	0.828	0.854	98.1947	0.158
1.788-1.861	0.222	77	0.193	1433	0.194	1533	0.707	0.799	98.4997	0.176
1.861-1.943	0.209	75	0.138	1355	0.141	1446	0.935	0.944	98.8935	0.134
1.943-2.038	0.188	94	0.13	1259	0.134	1367	0.955	0.964	98.9759	0.124
2.038-2.148	0.201	69	0.143	1243	0.145	1326	0.943	0.958	98.9442	0.144
2.148-2.278	0.188	40	0.152	1186	0.153	1236	0.957	0.955	99.1909	0.148
2.278-2.435	0.276	57	0.158	1129	0.163	1196	0.926	0.957	99.1639	0.154
2.435-2.629	0.225	52	0.175	1030	0.177	1089	0.939	0.948	99.3572	0.173
2.629-2.879	0.222	42	0.181	970	0.182	1015	0.946	0.946	99.7044	0.179
2.879-3.218	0.224	56	0.171	859	0.175	917	0.939	0.953	99.7819	0.176
3.218-3.713	0.2	40	0.182	761	0.183	801	0.954	0.96	100	0.19
3.713-4.541	0.197	33	0.154	660	0.156	693	0.961	0.969	100	0.166
4.541-6.394	0.331	23	0.185	522	0.189	545	0.903	0.961	100	0.202
6.394-48.533	0.188	13	0.22	301	0.218	314	0.944	0.926	100	0.226

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