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- PDB-4emb: Crystal structure of a phosphoglycerate mutase gpmA from Borrelia... -

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Basic information

Entry
Database: PDB / ID: 4emb
TitleCrystal structure of a phosphoglycerate mutase gpmA from Borrelia burgdorferi B31
Components2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
KeywordsISOMERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / lyme disease / tick-borne pathogen / 2-phosphoglycerate / 3-phosphoglycerate / glycolysis
Function / homology
Function and homology information


2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a phosphoglycerate mutase gpmA from Borrelia burgdorferi B31
Authors: Edwards, T.E. / Clifton, M.C. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionApr 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
B: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
C: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
D: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4548
Polymers126,2324
Non-polymers2224
Water7,296405
1
A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
C: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2404
Polymers63,1162
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
D: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2144
Polymers63,1162
Non-polymers982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6202
Polymers31,5581
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6202
Polymers31,5581
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6202
Polymers31,5581
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5932
Polymers31,5581
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.320, 116.750, 84.410
Angle α, β, γ (deg.)90.000, 107.670, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA5 - 24426 - 265
21GLUGLUBB5 - 24426 - 265
12ALAALAAA5 - 24726 - 268
22ALAALACC5 - 24726 - 268
13GLUGLUAA5 - 24426 - 265
23GLUGLUDD5 - 24426 - 265
14GLUGLUBB5 - 24426 - 265
24GLUGLUCC5 - 24426 - 265
15SERSERBB5 - 24526 - 266
25SERSERDD5 - 24526 - 266
16GLUGLUCC5 - 24426 - 265
26GLUGLUDD5 - 24426 - 265

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase / gpmA / BPG-dependent PGAM / PGAM / Phosphoglyceromutase / dPGM


Mass: 31558.045 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: B31 / Gene: BB_0658, gmpA, gpmA / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: O51602, EC: 5.4.2.1
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BobuA.01013.a.A1 selenomethionine-labeled PW26571 at 27.7 mg/mL against CSHT B6: 0.2 M magnesium acetate, 0.1 M sodium cacodylate, pH 6.5, 20% PEG8000, cryoprotectant: 20% ethylene glycol, ...Details: BobuA.01013.a.A1 selenomethionine-labeled PW26571 at 27.7 mg/mL against CSHT B6: 0.2 M magnesium acetate, 0.1 M sodium cacodylate, pH 6.5, 20% PEG8000, cryoprotectant: 20% ethylene glycol, crystal tracking ID 232024b6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 21, 2012
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 63486 / Num. obs: 63406 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 42.001 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.3-2.360.4734.7836086469799.9
2.36-2.420.3745.9634939454199.9
2.42-2.490.3236.9234279445199.8
2.49-2.570.287.76331944297100
2.57-2.660.2339.12322534177100
2.66-2.750.19110.72310364017100
2.75-2.850.1513.1830154390299.9
2.85-2.970.12115.7928854373699.9
2.97-3.10.10118.4927851360899.9
3.1-3.250.08521.626587344499.9
3.25-3.430.0725.6125311328499.8
3.43-3.640.06128.07236683075100
3.64-3.890.05730.6722541294799.8
3.89-4.20.05235.06205422698100
4.2-4.60.04737.6118955250299.9
4.6-5.140.04737.6717244227899.7
5.14-5.940.04836.8515102199599.8
5.94-7.270.04737.112793169899.9
7.27-10.290.04241.19888132999.6
10.290.04440.64495973097.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å47.6 Å
Translation3 Å47.6 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LNT

3lnt


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1995 / WRfactor Rwork: 0.1756 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8922 / SU B: 8.682 / SU ML: 0.112 / SU R Cruickshank DPI: 0.2205 / SU Rfree: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 3216 5.1 %RANDOM
Rwork0.1762 ---
obs0.1775 63405 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.91 Å2 / Biso mean: 38.1379 Å2 / Biso min: 16.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å2-0.2 Å2
2--2.26 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7600 0 13 405 8018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.027789
X-RAY DIFFRACTIONr_bond_other_d0.0060.025196
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.97610588
X-RAY DIFFRACTIONr_angle_other_deg1.174312707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6855971
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56724.294340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.229151281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9531541
X-RAY DIFFRACTIONr_chiral_restr0.0850.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218644
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021553
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: LOCAL / Weight: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms
11A90600.05
12B90600.05
21A89870.04
22C89870.04
31A88720.06
32D88720.06
41B90080.05
42C90080.05
51B90710.05
52D90710.05
61C89270.05
62D89270.05
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 237 -
Rwork0.225 4352 -
all-4589 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.43630.1034-0.31370.1499-0.26991.42140.0116-0.01470.0760.0186-0.0356-0.0775-0.0729-0.42190.0240.02310.01-0.0010.26420.05280.09211.5063.96953.9792
20.1532-0.0766-0.02270.57260.23120.86570.04630.03280.066-0.0338-0.0222-0.0220.04690.2523-0.02410.04230.01130.00810.11030.02890.1259-34.4878-5.9444-16.0033
30.47950.0077-0.27040.1352-0.2011.3039-0.00440.2112-0.04560.0274-0.0553-0.07690.1345-0.3050.05970.0753-0.0809-0.00650.20610.02510.069811.8326-11.9665-24.351
40.3057-0.2337-0.35380.63150.15370.76710.0564-0.15820.01420.0708-0.0184-0.01790.00750.222-0.0380.0893-0.0661-0.04270.12610.00260.0809-45.06041.79915.1139
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 249
2X-RAY DIFFRACTION2B5 - 245
3X-RAY DIFFRACTION3C5 - 248
4X-RAY DIFFRACTION4D5 - 245

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