PDB-4hjh: Iodide SAD phased crystal structure of a phosphoglucomutase from ...

ID or keywords:

Entry

Database: PDB / ID: 4hjh

Title

Iodide SAD phased crystal structure of a phosphoglucomutase from Brucella melitensis complexed with glucose-6-phosphate

Components

Phosphomannomutase

Keywords

ISOMERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Phosphoglucomutase / transferase / glucose-6-phosphate

Function / homology

Function and homology information

Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, conserved site ...
Similarity search - Domain/homology

Biological species

Brucella melitensis bv. 1 (bacteria)

Method

X-RAY DIFFRACTION /

SAD / Resolution: 2.1 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Iodide SAD phased crystal structure of a phosphoglucomutase from Brucella melitensis complexed with glucose-6-phosphate
Authors: Fairman, J.W. / Craig, T.K. / Staker, B.L.

History

Deposition	Oct 12, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 21, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Data collection / Category: pdbx_diffrn_reflns_shell / Item: _pdbx_diffrn_reflns_shell.percent_possible_obs
Revision 1.2	Oct 11, 2017	Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4hjh.cif.gz	356.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4hjh.ent.gz	300.1 KB	Display	PDB format
PDBx/mmJSON format	4hjh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4hjh_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4hjh_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4hjh_validation.xml.gz	42.7 KB	Display
Data in CIF	4hjh_validation.cif.gz	62.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hj/4hjh ftp://data.pdbj.org/pub/pdb/validation_reports/hj/4hjh	HTTPS FTP

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Related structure data

Similar structure data	1pcm-d 1p5g-d 6mnv-d 2fe6-d 4lv7-1 6n1e-d 2cib-d 3udz-3 3ebs-1 1akd-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 - HomologyF&H Search
Other databases	TargetTrack: SSGCID-BrmeA.01370.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phosphomannomutase

B: Phosphomannomutase

hetero molecules

113 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phosphomannomutase

hetero molecules

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

2

B: Phosphomannomutase

hetero molecules

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

Unit cell

Length a, b, c (Å)	61.950, 55.980, 131.670
Angle α, β, γ (deg.)	90.000, 92.180, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	0	1	0	A	4 - 475
2	0	1	0	B	4 - 475

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Protein , 1 types, 2 molecules AB

#1: Protein	Phosphomannomutase Mass: 51045.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis bv. 1 (bacteria) / Strain: 16M / Gene: BAWG_1686 / Production host: Escherichia coli (E. coli) / References: UniProt: D0B6G5, phosphomannomutase

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Non-polymers , 5 types, 691 molecules

#2: Chemical	... ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 75 / Source method: obtained synthetically / Formula: I
#3: Chemical	ChemComp-G6Q / GLUCOSE-6-PHOSPHATE Mass: 260.136 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C₆H₁₃O₉P
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.23 Å³/Da / Density % sol: 44.96 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Wizard III/IV well F10: PCB Buffer pH 7.0, 25% PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 28, 2012

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.54 Å / Relative weight: 1

Reflection

Number: 380712 / R_merge(I) obs: 0.075 / D res high: 2.1 Å / Num. obs: 102884 / % possible obs: 99.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs
2.1	2.15	7444	96.6	1	0.21
2.15	2.21	7433	99.9	1	0.199
2.21	2.28	7174	99.6	1	0.186
2.28	2.35	7048	99.9	1	0.161
2.35	2.42	6814	99.9	1	0.141
2.42	2.51	6582	100	1	0.126
2.51	2.6	6367	100	1	0.114
2.6	2.71	6111	99.9	1	0.104
2.71	2.83	5855	100	1	0.088
2.83	2.97	5621	99.9	1	0.081
2.97	3.13	5330	100	1	0.073
3.13	3.32	5043	100	1	0.062
3.32	3.55	4700	100	1	0.056
3.55	3.83	4395	100	1	0.05
3.83	4.2	4083	99.8	1	0.049
4.2	4.7	3687	100	1	0.047
4.7	5.42	3199	99.9	1	0.049
5.42	6.64	2735	99.9	1	0.052
6.64	9.39	2124	99.9	1	0.044

Reflection

Resolution: 2.1→50 Å / Num. all: 103194 / Num. obs: 102884 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 23.435 Å² / R_merge(I) obs: 0.075 / Net I/σ(I): 13.94

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	Diffraction-ID	% possible all
2.1-2.15	0.21	6.36	23359	7444	1	96.6
2.15-2.21	0.199	7.48	26884	7433	1	99.9
2.21-2.28	0.186	8.15	26134	7174	1	99.6
2.28-2.35	0.161	8.9	26141	7048	1	99.9
2.35-2.42	0.141	9.66	25408	6814	1	99.9
2.42-2.51	0.126	10.51	24678	6582	1	100
2.51-2.6	0.114	11.08	24010	6367	1	100
2.6-2.71	0.104	11.85	23060	6111	1	99.9
2.71-2.83	0.088	12.98	22192	5855	1	100
2.83-2.97	0.081	13.47	21441	5621	1	99.9
2.97-3.13	0.073	15.09	20271	5330	1	100
3.13-3.32	0.062	17.66	19241	5043	1	100
3.32-3.55	0.056	20.68	17778	4700	1	100
3.55-3.83	0.05	23.08	16498	4395	1	100
3.83-4.2	0.049	24.32	15308	4083	1	99.8
4.2-4.7	0.047	24.98	13869	3687	1	100
4.7-5.42	0.049	23.87	11981	3199	1	99.9
5.42-6.64	0.052	22.23	10325	2735	1	99.9
6.64-9.39	0.044	24.71	7963	2124	1	99.9

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
REFMAC	5.7.0029	refinement
PDB_EXTRACT	3.11	data extraction
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.1→46.01 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.918 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.649 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2086	2695	5.1 %	RANDOM
R_work	0.1736	-	-	-
all	0.1754	-	-	-
obs	0.1754	52960	99.79 %	-

Solvent computation

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

Displacement parameters

B_iso max: 73.93 Å² / B_iso mean: 20.401 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	0 Å²	-0.07 Å²
2-	-	-0.6 Å²	-0 Å²
3-	-	-	0.57 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→46.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6688	0	141	604	7433

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	6902
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	6521
X-RAY DIFFRACTION	r_angle_refined_deg	1.407	1.987	9418
X-RAY DIFFRACTION	r_angle_other_deg	0.922	3	14903
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.624	5	941
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.546	23.04	250
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.776	15	977
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.695	15	51
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	1126
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	7952
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1493

Refine LS restraints NCS

Ens-ID: 1 / Number: 26235 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.08 / Type: LOCAL / Weight: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 2.1→2.155 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.199	195	-
R_work	0.177	3631	-
all	-	3826	-
obs	-	-	97.5 %

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	2.384	-0.6496	-0.3252	1.6429	0.6053	2.1615	-0.0367	-0.4752	0.1159	0.1949	0.084	-0.0774	0.0059	0.0745	-0.0473	0.0528	-0.0159	-0.0403	0.1627	-0.0401	0.0754	52.7485	46.0246	25.376
2	1.4714	-0.183	-0.3717	1.3469	0.0484	2.2929	0.033	-0.0754	0.1758	0.0323	0.0117	-0.1226	-0.0339	0.183	-0.0447	0.0133	-0.0135	-0.0227	0.0634	-0.0237	0.1119	54.5172	45.0759	10.3841
3	1.4024	-0.3899	0.1162	1.6876	-0.5404	0.5561	0.0061	0.0735	0.097	-0.022	0.0025	0.0503	-0.0294	0.0455	-0.0086	0.007	-0.008	-0.0114	0.0454	0.0021	0.0571	41.9388	43.4342	0.5546
4	2.6319	0.5774	0.2288	1.3681	0.1627	1.8687	0.0443	-0.1449	-0.1871	0.1438	-0.008	0.0098	0.1995	0.047	-0.0363	0.0501	-0.0015	-0.0254	0.0365	0.019	0.0547	40.9764	27.5314	11.4942
5	1.2417	-0.4862	-0.3215	2.2623	0.5643	3.5196	0.0075	0.0125	-0.0633	-0.0458	0.0255	-0.1035	0.1527	0.0558	-0.033	0.015	-0.0124	-0.01	0.0551	-0.0078	0.082	52.2877	32.7	2.6088
6	1.9567	-0.3166	-0.8647	1.1136	0.8021	2.8988	0.0493	-0.1994	0.0192	0.0312	-0.0222	0.0259	-0.0765	-0.2423	-0.0271	0.0306	-0.0116	-0.0385	0.087	0.0307	0.0711	27.4528	39.6815	9.7401
7	2.5543	0.2025	1.109	2.1318	1.3328	2.8751	0.0917	-0.2295	-0.0688	0.0975	-0.1333	0.0392	-0.0197	-0.2296	0.0416	0.0152	-0.0065	-0.0086	0.0807	0.0053	0.0803	21.2445	39.6652	11.7519
8	2.3057	1.0497	0.6583	3.0371	0.8317	1.6654	-0.0586	0.1462	-0.0525	-0.3649	-0.1185	0.3968	-0.1672	-0.1143	0.1771	0.1604	0.0215	-0.1345	0.0814	-0.0553	0.1342	11.8466	15.5802	37.0856
9	3.4503	2.0276	0.7081	3.079	1.3386	0.6047	-0.2068	0.305	0.1157	-0.4154	0.0204	0.3863	-0.1965	-0.0441	0.1863	0.2756	0.0081	-0.149	0.1377	-0.0029	0.1008	13.9502	21.8244	37.0748
10	2.0874	1.3694	-0.5003	3.5634	-0.885	1.7942	-0.0154	0.0886	0.0129	-0.2656	0.1114	-0.2248	0.031	0.1952	-0.096	0.1099	-0.0085	0.0195	0.0808	-0.0453	0.0674	38.0819	17.0166	43.8773
11	2.1101	-0.5541	0.7668	0.9803	0.258	2.669	0.0562	0.001	-0.3232	-0.1853	0.0435	0.0184	0.1386	0.0303	-0.0997	0.1428	-0.0172	-0.0171	0.0266	0.0066	0.1174	29.2291	9.9772	56.1962
12	1.0848	-0.2602	0.3889	1.7858	0.4615	1.0291	-0.0361	0.1008	0.0693	-0.1673	0.0592	-0.0812	-0.1412	0.0715	-0.0231	0.1102	-0.0342	-0.0264	0.0432	0.0061	0.0746	28.0951	29.5653	51.7561
13	1.9565	0.8452	-0.0075	1.7688	0.2656	2.0655	0.0648	-0.1281	-0.0216	0.0944	-0.0947	0.1429	-0.0221	-0.3437	0.0299	0.1171	0.0173	-0.032	0.0722	0.0063	0.1001	13.0517	23.494	68.9184
14	18.0239	6.7188	0.6768	5.1411	0.1617	2.5771	0.059	-0.7231	-0.4561	0.1179	-0.179	-0.0529	0.3502	-0.2031	0.12	0.1693	-0.0086	-0.0149	0.076	0.0406	0.1038	16.6279	16.2446	73.9599

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 121
2	X-RAY DIFFRACTION	2	A	122 - 210
3	X-RAY DIFFRACTION	3	A	211 - 273
4	X-RAY DIFFRACTION	4	A	274 - 335
5	X-RAY DIFFRACTION	5	A	336 - 362
6	X-RAY DIFFRACTION	6	A	363 - 405
7	X-RAY DIFFRACTION	7	A	406 - 473
8	X-RAY DIFFRACTION	8	B	4 - 120
9	X-RAY DIFFRACTION	9	B	121 - 164
10	X-RAY DIFFRACTION	10	B	165 - 206
11	X-RAY DIFFRACTION	11	B	207 - 232
12	X-RAY DIFFRACTION	12	B	233 - 370
13	X-RAY DIFFRACTION	13	B	371 - 452
14	X-RAY DIFFRACTION	14	B	453 - 473

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