PDB-2amy: X-Ray Structure of Human Phosphomannomutase 2 (PMM2)

ID or keywords:

Entry

Database: PDB / ID: 2amy

Title

X-Ray Structure of Human Phosphomannomutase 2 (PMM2)

Components

Phosphomannomutase 2

Keywords

ISOMERASE / HS.459855 / HS.313504 / BC008310 / PHOSPHATASE / PFAM PF03332 / HAD SUPERFAMILY / JAECKEN DISEASE / CARBOHYDRATE-DEFICIENT GLYCOPROTEIN SYNDROME / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / Center for Eukaryotic Structural Genomics

Function / homology

Function and homology information

Defective PMM2 causes PMM2-CDG / Synthesis of GDP-mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / protein glycosylation / neuronal cell body / nucleoplasm ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.09 Å

Authors

Wesenberg, G.E. / Phillips Jr., G.N. / McCoy, J.G. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: To be Published
Title: X-Ray Structure of Human Phosphomannomutase 2 (PMM2)
Authors: Center for Eukaryotic Structural Genomics (CESG)

History

Deposition	Aug 10, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 23, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 11, 2017	Group: Refinement description / Category: software
Revision 1.4	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2amy.cif.gz	64.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2amy.ent.gz	49.4 KB	Display	PDB format
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Validation report

Summary document	2amy_validation.pdf.gz	454.8 KB	Display	wwPDB validaton report
Full document	2amy_full_validation.pdf.gz	458.4 KB	Display
Data in XML	2amy_validation.xml.gz	13.2 KB	Display
Data in CIF	2amy_validation.cif.gz	18.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/am/2amy ftp://data.pdbj.org/pub/pdb/validation_reports/am/2amy	HTTPS FTP

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Related structure data

Similar structure data	2q4r-d 3ajz-1 1no5-5 4dwn-d 3d8t-2 2cbf-d 3d8r-d 4e16-d 6b94-d 3u58-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: GO.36653

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Phosphomannomutase 2

hetero molecules

28.6 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)	70.622, 70.622, 100.150
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-449- HOH

#1: Protein	Phosphomannomutase 2 / PMM 2 Mass: 28263.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HS.459855 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: O15305, phosphomannomutase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.6	51.9
2	2.6	51.9

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
277	1	vapor diffusion, hanging drop	8.5	10 MG/ML PROTEIN, 24 % W/V PEG 2K, 0.12 M GLYCINE, 0.1 M TRIETHANOLAMINE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
277	2	vapor diffusion, hanging drop	8.5	10 MG/ML PROTEIN, 24 % W/V PEG 2K, 0.12 M GLYCINE, 0.1 M TRIETHANOLAMINE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3		1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	22-BM	1	0.97243
SYNCHROTRON	APS	22-ID	2	0.97625, 0.97947

Detector

Type	ID	Detector	Date	Details
MARMOSAIC 225 mm CCD	1	CCD	Jul 11, 2005	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
MARMOSAIC 300 mm CCD	2	CCD	Jun 13, 2005	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	WATER COOLED SI (111) DOUBLE BOUNCE	SINGLE WAVELENGTH	M	x-ray	1
2	CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE	MAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97243	1
2	0.97625	1
3	0.97947	1

Reflection

D res low: 50 Å

Redundancy (%)	ID	Number	R_merge(I) obs	Χ²	D res high (Å)	% possible obs
12.3	1	17547	0.069	1.082	2.09	99
19.1	2	23287	0.067	1.207	1.86	94.4
12.7	3	22600	0.072	1.308	1.86	92.5

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.5	50	98.7	1	0.051	1.136	12.1
3.57	4.5	100	1	0.06	1.08	12.9
3.12	3.57	100	1	0.06	1.249	13.1
2.84	3.12	100	1	0.087	1.14	13.1
2.63	2.84	100	1	0.127	1.123	13.1
2.48	2.63	100	1	0.192	1.005	13.3
2.35	2.48	100	1	0.292	0.977	13.1
2.25	2.35	100	1	0.413	1.022	12.9
2.16	2.25	100	1	0.519	1.091	11.3
2.09	2.16	91.5	1	0.599	0.888	7
4.01	50	99.2	2	0.055	1.69	20.2
3.18	4.01	100	2	0.061	1.27	21.6
2.78	3.18	100	2	0.07	1.24	21.9
2.52	2.78	100	2	0.098	1.187	21.9
2.34	2.52	100	2	0.139	1.203	22
2.21	2.34	100	2	0.198	1.087	21.9
2.09	2.21	100	2	0.293	1.03	21.3
2	2.09	99.8	2	0.445	0.968	16.9
1.93	2	87.9	2	0.496	0.924	9.9
1.86	1.93	56	2	0.553	1.404	7
4.01	50	98.6	3	0.061	1.936	13.6
3.18	4.01	100	3	0.063	1.489	14.4
2.78	3.18	100	3	0.075	1.4	14.6
2.52	2.78	100	3	0.105	1.219	14.6
2.34	2.52	100	3	0.153	1.237	14.6
2.21	2.34	100	3	0.227	1.115	14.6
2.09	2.21	100	3	0.33	1.057	13.9
2	2.09	98	3	0.493	1.036	10.4
1.93	2	79.4	3	0.527	1.021	5.9
1.86	1.93	47.9	3	0.555	0.952	4.1

Reflection

Resolution: 2.09→50 Å / Num. obs: 17547 / % possible obs: 99 % / Redundancy: 12.3 % / R_merge(I) obs: 0.069 / Χ²: 1.082 / Net I/σ(I): 20.356

Reflection scale

Group code: 1

Reflection shell

Resolution: 2.09→2.16 Å / % possible obs: 91.5 % / Redundancy: 7 % / R_merge(I) obs: 0.599 / Mean I/σ(I) obs: 3.031 / Num. measured obs: 1575 / Χ²: 0.888 / % possible all: 91.5

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Phasing

Phasing

Method:

MAD

Phasing MAD set

Highest resolution: 1.86 Å / Lowest resolution: 30.46 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	20527	2513
ISO_2	0.695	0.628	1.646	1.418	19600	2478
ANO_1	0.666	0	1.53	0	19775	0
ANO_2	0.794	0	0.562	0	18817	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	8.04-30.46	0	0	0	0	210	118
ISO_1	5.79-8.04	0	0	0	0	409	133
ISO_1	4.76-5.79	0	0	0	0	552	122
ISO_1	4.13-4.76	0	0	0	0	651	136
ISO_1	3.7-4.13	0	0	0	0	743	131
ISO_1	3.38-3.7	0	0	0	0	853	127
ISO_1	3.14-3.38	0	0	0	0	916	142
ISO_1	2.94-3.14	0	0	0	0	994	115
ISO_1	2.77-2.94	0	0	0	0	1062	127
ISO_1	2.63-2.77	0	0	0	0	1134	123
ISO_1	2.51-2.63	0	0	0	0	1181	117
ISO_1	2.4-2.51	0	0	0	0	1249	133
ISO_1	2.31-2.4	0	0	0	0	1305	137
ISO_1	2.22-2.31	0	0	0	0	1337	129
ISO_1	2.15-2.22	0	0	0	0	1407	144
ISO_1	2.08-2.15	0	0	0	0	1446	129
ISO_1	2.02-2.08	0	0	0	0	1484	135
ISO_1	1.96-2.02	0	0	0	0	1468	124
ISO_1	1.91-1.96	0	0	0	0	1218	115
ISO_1	1.86-1.91	0	0	0	0	908	76
ANO_1	8.04-30.46	0.543	0	1.891	0	210	0
ANO_1	5.79-8.04	0.343	0	3.533	0	409	0
ANO_1	4.76-5.79	0.406	0	2.93	0	552	0
ANO_1	4.13-4.76	0.525	0	2.387	0	651	0
ANO_1	3.7-4.13	0.539	0	2.257	0	743	0
ANO_1	3.38-3.7	0.565	0	2.133	0	853	0
ANO_1	3.14-3.38	0.554	0	2.233	0	916	0
ANO_1	2.94-3.14	0.532	0	2.242	0	994	0
ANO_1	2.77-2.94	0.611	0	2.013	0	1062	0
ANO_1	2.63-2.77	0.671	0	1.539	0	1134	0
ANO_1	2.51-2.63	0.741	0	1.252	0	1181	0
ANO_1	2.4-2.51	0.819	0	1.054	0	1249	0
ANO_1	2.31-2.4	0.87	0	0.756	0	1305	0
ANO_1	2.22-2.31	0.918	0	0.617	0	1337	0
ANO_1	2.15-2.22	0.945	0	0.455	0	1407	0
ANO_1	2.08-2.15	0.971	0	0.349	0	1446	0
ANO_1	2.02-2.08	0.986	0	0.268	0	1473	0
ANO_1	1.96-2.02	0.995	0	0.217	0	1332	0
ANO_1	1.91-1.96	0.996	0	0.202	0	924	0
ANO_1	1.86-1.91	0.998	0	0.183	0	597	0
ISO_2	8.04-30.46	0.476	0.477	2.643	1.86	210	113
ISO_2	5.79-8.04	0.465	0.531	3.203	1.979	409	132
ISO_2	4.76-5.79	0.568	0.556	2.535	1.992	552	122
ISO_2	4.13-4.76	0.667	0.622	1.812	1.412	651	136
ISO_2	3.7-4.13	0.73	0.741	1.666	1.162	743	131
ISO_2	3.38-3.7	0.698	0.714	1.519	1.069	853	127
ISO_2	3.14-3.38	0.689	0.707	1.634	1.143	916	142
ISO_2	2.94-3.14	0.709	0.712	1.677	1.139	994	115
ISO_2	2.77-2.94	0.728	0.735	1.626	1.044	1062	127
ISO_2	2.63-2.77	0.745	0.796	1.513	0.995	1134	123
ISO_2	2.51-2.63	0.761	0.822	1.335	1.003	1181	117
ISO_2	2.4-2.51	0.795	0.787	1.15	0.807	1249	133
ISO_2	2.31-2.4	0.834	0.786	0.983	0.655	1305	137
ISO_2	2.22-2.31	0.864	0.888	0.833	0.556	1337	129
ISO_2	2.15-2.22	0.862	0.891	0.645	0.439	1407	144
ISO_2	2.08-2.15	0.885	0.971	0.52	0.4	1445	128
ISO_2	2.02-2.08	0.895	0.95	0.389	0.311	1450	132
ISO_2	1.96-2.02	0.926	1.021	0.284	0.231	1292	121
ISO_2	1.91-1.96	0.97	1.008	0.248	0.169	894	107
ISO_2	1.86-1.91	0.967	1.035	0.207	0.169	516	62
ANO_2	8.04-30.46	0.756	0	0.566	0	210	0
ANO_2	5.79-8.04	0.674	0	0.733	0	409	0
ANO_2	4.76-5.79	0.69	0	0.721	0	552	0
ANO_2	4.13-4.76	0.728	0	0.741	0	651	0
ANO_2	3.7-4.13	0.723	0	0.729	0	743	0
ANO_2	3.38-3.7	0.749	0	0.711	0	853	0
ANO_2	3.14-3.38	0.753	0	0.69	0	916	0
ANO_2	2.94-3.14	0.751	0	0.7	0	994	0
ANO_2	2.77-2.94	0.787	0	0.622	0	1062	0
ANO_2	2.63-2.77	0.827	0	0.56	0	1134	0
ANO_2	2.51-2.63	0.873	0	0.482	0	1181	0
ANO_2	2.4-2.51	0.921	0	0.382	0	1249	0
ANO_2	2.31-2.4	0.946	0	0.297	0	1305	0
ANO_2	2.22-2.31	0.967	0	0.238	0	1337	0
ANO_2	2.15-2.22	0.983	0	0.18	0	1407	0
ANO_2	2.08-2.15	0.991	0	0.149	0	1432	0
ANO_2	2.02-2.08	0.997	0	0.125	0	1391	0
ANO_2	1.96-2.02	0.997	0	0.109	0	1056	0
ANO_2	1.91-1.96	0.997	0	0.102	0	607	0
ANO_2	1.86-1.91	0.998	0	0.086	0	328	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-4.265	24.304	22.314	SE	43.73	2.03
2	-4.9	29.164	81.59	SE	52.98	2.03
3	-2.632	35.606	35.355	SE	72.19	1.38
4	-11.231	41.784	52.929	SE	55.96	0.91

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 23254

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.03-100	50.6	0.924	502
5.53-7.03	47	0.949	518
4.82-5.53	45.1	0.953	505
4.35-4.82	45.3	0.942	522
3.99-4.35	49.1	0.924	581
3.71-3.99	51.8	0.925	603
3.48-3.71	50.9	0.921	671
3.29-3.48	50.9	0.914	693
3.13-3.29	54.5	0.904	737
2.99-3.13	53	0.895	768
2.87-2.99	54	0.881	804
2.76-2.87	52.9	0.891	837
2.66-2.76	53.6	0.868	854
2.57-2.66	55.6	0.87	891
2.49-2.57	53.9	0.861	909
2.42-2.49	64.8	0.859	955
2.35-2.42	61.5	0.856	946
2.29-2.35	65.2	0.852	1013
2.23-2.29	67	0.845	1029
2.18-2.23	66.9	0.843	1018
2.13-2.18	71.7	0.852	1069
2.09-2.13	78.9	0.849	1118
2.04-2.09	80.9	0.84	1121
2-2.04	80.6	0.832	1108
1.96-2	82.9	0.805	1111
1.93-1.96	82.4	0.717	984
1.89-1.93	87.3	0.694	786
1.86-1.89	85.2	0.607	601

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	1.7	data extraction
SOLOMON		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MAD / Resolution: 2.09→38.745 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.934 / SU B: 12.513 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SELENIUM C COEFFICIENT FOR STRUCTURE FACTOR CALCULATION SET TO -9.00, MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.272	924	5.3 %	RANDOM
R_work	0.199	-	-	-
all	0.202	-	-	-
obs	0.20226	17514	99.49 %	-

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 mean: 56.423 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.79 Å²	0.39 Å²	0 Å²
2-	-	0.79 Å²	0 Å²
3-	-	-	-1.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.09→38.745 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1943	0	19	142	2104

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	2001
X-RAY DIFFRACTION	r_angle_refined_deg	1.821	1.975	2681
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.85	5	238
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.427	24.257	101
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.162	15	370
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.44	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.135	0.2	283
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1518
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.2	943
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	1378
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.203	0.2	124
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.246	0.2	37
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.203	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	1.838	2	1250
X-RAY DIFFRACTION	r_mcangle_it	3.005	4	1930
X-RAY DIFFRACTION	r_scbond_it	5.216	6	865
X-RAY DIFFRACTION	r_scangle_it	6.65	8	751

LS refinement shell

Resolution: 2.091→2.146 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.297	90	-
R_work	0.235	1138	-
all	-	1228	-
obs	-	-	95.19 %

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	4.8606	-1.5799	0.3934	3.851	0.2416	2.5112	-0.1111	0.2731	0.2499	0.0242	0.0396	-0.211	-0.4915	0.385	0.0715	-0.0125	-0.3528	-0.035	-0.0203	0.0297	-0.2456	41.5435	-9.8874	-3.8083
2	1.2239	0.2332	-0.6967	1.4339	2.3094	5.0062	-0.2582	0.0865	-0.0931	0.1429	0.0069	0.3586	0.416	0.1641	0.2513	0.0287	-0.059	-0.0065	-0.3065	0.0652	-0.0677	16.4164	-8.8753	9.4686
3	4.5858	-1.0498	0.202	5.5761	-0.7216	2.5763	0.0527	0.3304	-0.4978	-0.1983	0.0803	0.3414	-0.1696	0.1776	-0.133	-0.1345	-0.2446	-0.0313	-0.0581	-0.0617	-0.2002	36.0691	-22.2711	-7.1268

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Auth seq-ID	Label seq-ID
1	1	4 - 84	4 - 84
2	2	85 - 198	85 - 198
3	3	199 - 246	199 - 246

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