PDB-3emj: 2.2 A crystal structure of inorganic pyrophosphatase from rickett...

ID or keywords:

Entry

Database: PDB / ID: 3emj

Title

2.2 A crystal structure of inorganic pyrophosphatase from rickettsia prowazekii (p21 form)

Components

Inorganic pyrophosphatase

Keywords

HYDROLASE / RICKETTSIA / INORGANIC PYROPHOSPHATASE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID / Cytoplasm / Magnesium / Metal-binding

Function / homology

Function and homology information

inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function

Biological species

Rickettsia prowazekii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: 2.2 A crystal structure of inorganic pyrophosphatase from rickettsia prowazekii (p21 form)
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)

History

Deposition	Sep 24, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 7, 2008	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 ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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	3emj.cif.gz	392.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3emj.ent.gz	323.9 KB	Display	PDB format
PDBx/mmJSON format	3emj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3emj_validation.pdf.gz	551.8 KB	Display	wwPDB validaton report
Full document	3emj_full_validation.pdf.gz	619.2 KB	Display
Data in XML	3emj_validation.xml.gz	79.9 KB	Display
Data in CIF	3emj_validation.cif.gz	107.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/em/3emj ftp://data.pdbj.org/pub/pdb/validation_reports/em/3emj	HTTPS FTP

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Related structure data

Similar structure data	3d53-d 1qez-d 3sw5-d 3r6e-d 2bqx-1 1mjz-1 1obw-1 3ld3-1 1ude-1 1ygz-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Inorganic pyrophosphatase

B: Inorganic pyrophosphatase

C: Inorganic pyrophosphatase

D: Inorganic pyrophosphatase

E: Inorganic pyrophosphatase

F: Inorganic pyrophosphatase

G: Inorganic pyrophosphatase

H: Inorganic pyrophosphatase

I: Inorganic pyrophosphatase

J: Inorganic pyrophosphatase

K: Inorganic pyrophosphatase

L: Inorganic pyrophosphatase

hetero molecules

236 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Inorganic pyrophosphatase

B: Inorganic pyrophosphatase

C: Inorganic pyrophosphatase

D: Inorganic pyrophosphatase

E: Inorganic pyrophosphatase

F: Inorganic pyrophosphatase

hetero molecules

defined by author&software
118 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Inorganic pyrophosphatase

H: Inorganic pyrophosphatase

I: Inorganic pyrophosphatase

J: Inorganic pyrophosphatase

K: Inorganic pyrophosphatase

L: Inorganic pyrophosphatase

hetero molecules

defined by author&software
118 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.960, 107.350, 128.420
Angle α, β, γ (deg.)	90.000, 96.050, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	ARG	ARG	A	A	14 - 171	15 - 172
2	1	GLU	GLU	ARG	ARG	C	C	14 - 171	15 - 172
3	1	GLU	GLU	ARG	ARG	E	E	14 - 171	15 - 172
1	2	ASN	ASN	ARG	ARG	B	B	13 - 171	14 - 172
2	2	ASN	ASN	ARG	ARG	D	D	13 - 171	14 - 172
3	2	ASN	ASN	ARG	ARG	F	F	13 - 171	14 - 172
1	3	ASN	ASN	ARG	ARG	G	G	13 - 171	14 - 172
2	3	ASN	ASN	ARG	ARG	H	H	13 - 171	14 - 172
3	3	ASN	ASN	ARG	ARG	I	I	13 - 171	14 - 172
1	4	GLU	GLU	ARG	ARG	J	J	14 - 171	15 - 172
2	4	GLU	GLU	ARG	ARG	K	K	14 - 171	15 - 172
3	4	GLU	GLU	ARG	ARG	L	L	14 - 171	15 - 172
1	5	ASN	ASN	ASN	ASN	A	A	13 - 172	14 - 173
2	5	ASN	ASN	ASN	ASN	F	F	13 - 172	14 - 173
1	6	ILE	ILE	ARG	ARG	B	B	6 - 171	7 - 172
2	6	ILE	ILE	ARG	ARG	C	C	6 - 171	7 - 172
1	7	GLU	GLU	ARG	ARG	D	D	14 - 171	15 - 172
2	7	GLU	GLU	ARG	ARG	E	E	14 - 171	15 - 172
1	8	ILE	ILE	ARG	ARG	G	G	6 - 171	7 - 172
2	8	ILE	ILE	ARG	ARG	J	J	6 - 171	7 - 172
1	9	ILE	ILE	ARG	ARG	H	H	6 - 171	7 - 172
2	9	ILE	ILE	ARG	ARG	K	K	6 - 171	7 - 172
1	10	GLU	GLU	ARG	ARG	I	I	14 - 171	15 - 172
2	10	GLU	GLU	ARG	ARG	L	L	14 - 171	15 - 172
1	11	ILE	ILE	ASN	ASN	C	C	6 - 172	7 - 173
2	11	ILE	ILE	ASN	ASN	K	K	6 - 172	7 - 173
1	12	ILE	ILE	ASN	ASN	A	A	6 - 172	7 - 173
2	12	ILE	ILE	ASN	ASN	J	J	6 - 172	7 - 173
1	13	PHE	PHE	ARG	ARG	D	D	2 - 171	3 - 172
2	13	PHE	PHE	ARG	ARG	H	H	2 - 171	3 - 172
1	14	ILE	ILE	ARG	ARG	B	B	6 - 171	7 - 172
2	14	ILE	ILE	ARG	ARG	G	G	6 - 171	7 - 172
1	15	GLU	GLU	ARG	ARG	E	E	14 - 171	15 - 172
2	15	GLU	GLU	ARG	ARG	L	L	14 - 171	15 - 172
1	16	ASN	ASN	ASN	ASN	F	F	13 - 172	14 - 173
2	16	ASN	ASN	ASN	ASN	I	I	13 - 172	14 - 173

NCS ensembles :

#1: Protein	Inorganic pyrophosphatase / Pyrophosphate phospho-hydrolase / PPase Mass: 19629.762 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rickettsia prowazekii (bacteria) / Strain: MADRID E / Gene: ppa, RP589 / Plasmid: pET28-SMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZCW5, inorganic diphosphatase
#2: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.36 Å³/Da / Density % sol: 47.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 10.5 Details: 30% PEG 400, 100 mM CAPS, pH 10.5, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.977408 Å

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS

Radiation

Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.977408 Å / Relative weight: 1

Reflection

Resolution: 2.2→128.037 Å / Num. all: 330779 / Num. obs: 103788 / % possible obs: 93.6 % / Redundancy: 3.2 % / R_merge(I) obs: 0.07 / R_sym value: 0.07 / Net I/σ(I): 8.689

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	R_sym value	% possible all
2.2-2.32	3.1	0.51	1.4	0.51	88.5
2.32-2.46	3.1	0.377	2	0.377	89.7
2.46-2.63	3.1	0.277	2.4	0.277	90.9
2.63-2.84	3.1	0.169	4.3	0.169	92.8
2.84-3.11	3.1	0.102	7	0.102	94.7
3.11-3.48	3.1	0.063	10.6	0.063	96.2
3.48-4.02	3.3	0.044	13.7	0.044	98.3
4.02-4.92	3.6	0.036	15.5	0.036	99.7
4.92-6.96	3.6	0.031	17.9	0.031	100
6.96-36.99	3.3	0.03	15.7	0.03	98.4

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.55 Å	29.95 Å
Translation	2.55 Å	29.95 Å

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Processing

Software

Name	Version	Classification
SCALA	3.2.25	data scaling
MOLREP		phasing
REFMAC	refmac_5.4.0069	refinement
PDB_EXTRACT	3.006	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.555 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26659	5260	5.1 %	RANDOM
R_work	0.22733	-	-	-
obs	0.22934	98484	93.66 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 40.172 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.01 Å²	0 Å²	-0.35 Å²
2-	-	-1.34 Å²	0 Å²
3-	-	-	0.26 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15743	0	26	420	16189

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	16110
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	11066
X-RAY DIFFRACTION	r_angle_refined_deg	1.826	1.971	21750
X-RAY DIFFRACTION	r_angle_other_deg	1.222	3	27291
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.295	5	1982
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.354	25.471	700
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.527	15	3033
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.196	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	2441
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	17479
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2938
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	0.835	1.5	9866
X-RAY DIFFRACTION	r_mcbond_other	0.252	1.5	3988
X-RAY DIFFRACTION	r_mcangle_it	1.517	2	16107
X-RAY DIFFRACTION	r_scbond_it	2.174	3	6244
X-RAY DIFFRACTION	r_scangle_it	3.451	4.5	5635
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	2112	MEDIUM POSITIONAL	0.47	0.5
1	C	2112	MEDIUM POSITIONAL	0.38	0.5
1	E	2112	MEDIUM POSITIONAL	0.5	0.5
1	A	2112	MEDIUM THERMAL	0.78	2
1	C	2112	MEDIUM THERMAL	0.79	2
1	E	2112	MEDIUM THERMAL	0.86	2
2	B	2099	MEDIUM POSITIONAL	0.51	0.5
2	D	2099	MEDIUM POSITIONAL	0.51	0.5
2	F	2099	MEDIUM POSITIONAL	0.53	0.5
2	B	2099	MEDIUM THERMAL	0.73	2
2	D	2099	MEDIUM THERMAL	0.62	2
2	F	2099	MEDIUM THERMAL	0.7	2
3	G	2123	MEDIUM POSITIONAL	0.49	0.5
3	H	2123	MEDIUM POSITIONAL	0.52	0.5
3	I	2123	MEDIUM POSITIONAL	0.52	0.5
3	G	2123	MEDIUM THERMAL	0.93	2
3	H	2123	MEDIUM THERMAL	0.7	2
3	I	2123	MEDIUM THERMAL	0.77	2
4	J	2124	MEDIUM POSITIONAL	0.42	0.5
4	K	2124	MEDIUM POSITIONAL	0.41	0.5
4	L	2124	MEDIUM POSITIONAL	0.48	0.5
4	J	2124	MEDIUM THERMAL	0.8	2
4	K	2124	MEDIUM THERMAL	0.83	2
4	L	2124	MEDIUM THERMAL	0.85	2
5	A	2129	MEDIUM POSITIONAL	0.45	0.5
5	A	2129	MEDIUM THERMAL	1.39	2
6	B	2190	MEDIUM POSITIONAL	0.4	0.5
6	B	2190	MEDIUM THERMAL	1.17	2
7	D	2093	MEDIUM POSITIONAL	0.46	0.5
7	D	2093	MEDIUM THERMAL	1.24	2
8	G	2202	MEDIUM POSITIONAL	0.47	0.5
8	G	2202	MEDIUM THERMAL	1.37	2
9	H	2213	MEDIUM POSITIONAL	0.46	0.5
9	H	2213	MEDIUM THERMAL	1.01	2
10	I	2122	MEDIUM POSITIONAL	0.51	0.5
10	I	2122	MEDIUM THERMAL	1.13	2
11	C	2248	MEDIUM POSITIONAL	0.24	0.5
11	C	2248	MEDIUM THERMAL	0.45	2
12	A	2237	MEDIUM POSITIONAL	0.2	0.5
12	A	2237	MEDIUM THERMAL	0.53	2
13	D	2275	MEDIUM POSITIONAL	0.23	0.5
13	D	2275	MEDIUM THERMAL	0.36	2
14	B	2225	MEDIUM POSITIONAL	0.24	0.5
14	B	2225	MEDIUM THERMAL	0.68	2
15	E	2135	MEDIUM POSITIONAL	0.38	0.5
15	E	2135	MEDIUM THERMAL	0.48	2
16	F	2150	MEDIUM POSITIONAL	0.22	0.5
16	F	2150	MEDIUM THERMAL	0.38	2

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.355	391	-
R_work	0.3	6769	-
obs	-	-	88.36 %

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