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- PDB-3nvl: Crystal Structure of Phosphoglycerate Mutase from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 3nvl
TitleCrystal Structure of Phosphoglycerate Mutase from Trypanosoma brucei
Components2,3-bisphosphoglycerate-independent phosphoglycerate mutase
KeywordsISOMERASE
Function / homology
Function and homology information


phosphoglycerate mutase (2,3-diphosphoglycerate-independent) / phosphoglycerate mutase activity / glucose catabolic process / ciliary plasm / gluconeogenesis / glycolytic process / manganese ion binding / carbohydrate metabolic process / nucleoplasm / identical protein binding ...phosphoglycerate mutase (2,3-diphosphoglycerate-independent) / phosphoglycerate mutase activity / glucose catabolic process / ciliary plasm / gluconeogenesis / glycolytic process / manganese ion binding / carbohydrate metabolic process / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain / BPG-independent phosphoglycerate mutase, domain B / Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent / BPG-independent PGAM, N-terminal / BPG-independent phosphoglycerate mutase, domain B superfamily / BPG-independent PGAM N-terminus (iPGM_N) / Metalloenzyme / Metalloenzyme superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A ...2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain / BPG-independent phosphoglycerate mutase, domain B / Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent / BPG-independent PGAM, N-terminal / BPG-independent phosphoglycerate mutase, domain B superfamily / BPG-independent PGAM N-terminus (iPGM_N) / Metalloenzyme / Metalloenzyme superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsMercaldi, G.F. / Pereira, H.M. / Cordeiro, A.T. / Andricopulo, A.D. / Thiemann, O.H.
CitationJournal: Febs J. / Year: 2012
Title: Crystal structure of phosphoglycerate mutase from Trypanosoma brucei.
Authors: Mercaldi, G.F. / Pereira, H.M. / Cordeiro, A.T. / Michels, P.A. / Thiemann, O.H.
History
DepositionJul 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
B: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,1358
Polymers125,7082
Non-polymers4286
Water4,270237
1
A: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0684
Polymers62,8541
Non-polymers2143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0684
Polymers62,8541
Non-polymers2143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.670, 85.660, 109.110
Angle α, β, γ (deg.)90.00, 102.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2,3-bisphosphoglycerate-independent phosphoglycerate mutase


Mass: 62853.773 Da / Num. of mol.: 2 / Fragment: PGAM (UNP RESIDUES 1-551)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: TREU927 / Gene: Tb10.6k15.2620 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38AH1, EC: 5.4.2.1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.05M ammonium sulfate, 0.1 M Bis-Tris, and 25% (w/v) PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.3→106.646 Å / Num. all: 46642 / Num. obs: 46642 / % possible obs: 92.7 % / Redundancy: 4.2 % / Rsym value: 0.1 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.424.40.6641.12644060660.66482.8
2.42-2.574.30.4811.52505858080.48184.1
2.57-2.754.20.3461.72384857130.34687.8
2.75-2.974.10.2213.42313956910.22193.5
2.97-3.2540.1415.22202354410.14198.1
3.25-3.644.20.0917.62126250790.091100
3.64-4.24.30.0768.71911544840.076100
4.2-5.144.30.0610.91616537650.06100
5.14-7.274.30.05611.51260229510.056100
7.27-35.5494.20.04115.3683416440.04198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
MOLREPphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IGY

3igy


Resolution: 2.3→35.549 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.33 / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2166 2271 5.1 %
Rwork0.1658 --
obs0.1684 44536 88.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.089 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 147.26 Å2 / Biso mean: 42.798 Å2 / Biso min: 11.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.686 Å20 Å25.2629 Å2
2---0.206 Å2-0 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8498 0 14 237 8749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048686
X-RAY DIFFRACTIONf_angle_d0.80111742
X-RAY DIFFRACTIONf_chiral_restr0.0581272
X-RAY DIFFRACTIONf_plane_restr0.0031568
X-RAY DIFFRACTIONf_dihedral_angle_d16.4833206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35010.34981090.2432163227273
2.3501-2.40470.3028970.23152171226872
2.4047-2.46480.3251210.22242226234776
2.4648-2.53150.2991450.21392242238776
2.5315-2.60590.27471340.20292311244578
2.6059-2.690.26711300.20382428255882
2.69-2.78610.26061450.19792509265485
2.7861-2.89760.25631460.19962647279389
2.8976-3.02940.29021630.19382767293093
3.0294-3.18910.23131370.17852845298296
3.1891-3.38870.2461640.16452951311599
3.3887-3.65010.18951490.14592972312199
3.6501-4.0170.16441580.13129423100100
4.017-4.59720.14871640.119530163180100
4.5972-5.78790.16781520.139830163168100
5.7879-35.55270.20851570.161330593216100
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3994-0.08710.04021.0267-0.30610.40690.0141-0.0363-0.0134-0.0161-0.0130.00610.07180.01090.11520.02510.00290.088-0.00890.0457-2.7436-11.085919.4918
21.3240.3407-0.74620.4107-0.26790.95940.0319-0.0610.01780.1199-0.02930.01330.0375-0.0570.12030.0465-0.01540.1397-0.07030.1764-43.949422.300533.9636
30.0850.0769-0.07850.03360.02610.13050.0122-0.02920.12510.0329-0.0099-0.0345-0.03260.01650.20820.0459-0.030.2063-0.01730.1873-20.83994.507627.137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:551 OR RESID 552:554 ) )A3 - 551
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:551 OR RESID 552:554 ) )A552 - 554
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 3:551 OR RESID 552:554 ) )B3 - 551
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 3:551 OR RESID 552:554 ) )B552 - 554
5X-RAY DIFFRACTION3( CHAIN A AND RESID 555:696 ) OR ( CHAIN B AND RESID 555:649 )A555 - 696
6X-RAY DIFFRACTION3( CHAIN A AND RESID 555:696 ) OR ( CHAIN B AND RESID 555:649 )B555 - 649

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