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- PDB-5vpu: Crystal Structure of 2,3-bisphosphoglycerate-independent phosphog... -

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Basic information

Entry
Database: PDB / ID: 5vpu
TitleCrystal Structure of 2,3-bisphosphoglycerate-independent phosphoglycerate mutase bound to 3-phosphoglycerate, from Acinetobacter baumannii
Components2,3-bisphosphoglycerate-independent phosphoglycerate mutase
KeywordsISOMERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


: / phosphoglycerate mutase (2,3-diphosphoglycerate-independent) / glucose catabolic process / glycolytic process / manganese ion binding / 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-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / ACETATE ION / : / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of 2,3-bisphosphoglycerate-independent phosphoglycerate mutase bound to 3-phosphoglycerate, from Acinetobacter baumannii
Authors: Delker, S.L. / Dranow, D.M. / Abendroth, J. / Lorimer, D. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMay 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation_author
Item: _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,25013
Polymers57,4021
Non-polymers84812
Water12,611700
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.940, 82.090, 72.410
Angle α, β, γ (deg.)90.00, 97.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 57401.840 Da / Num. of mol.: 1 / Fragment: AcbaC.17275.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: gpmI, A7M79_08915, A8A08_04445, A8G88_07785, AB895_1730, AB988_1552, ABUW_3643, APD31_01565, APD31_14450, IX87_15700
Plasmid: AcbaC.17275.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A059ZPG7, phosphoglycerate mutase (2,3-diphosphoglycerate-independent)

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Non-polymers , 5 types, 712 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MCSG1 F2: 0.2 M Ammonium Acetate 0.1 M Bis-Tris: HCl, pH 6.5 25 % (w/v) PEG 3350 +3mM 3-phosphoglycerate cryo:15% Ethylene glycol PS38071 24.7mg/mL, 0.4+0.4 puck frn7-12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 29, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→41.045 Å / Num. obs: 84305 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.142 % / Biso Wilson estimate: 12.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.052 / Χ2: 1.066 / Net I/σ(I): 22.98 / Num. measured all: 517771 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.545.1480.1519.0560260.9870.16995.5
1.54-1.586.0520.13111.3460210.9920.14398.6
1.58-1.636.0750.11812.7258360.9930.12998.7
1.63-1.686.0040.10613.8357570.9940.11698.9
1.68-1.735.7140.09115.1755050.9950.199.1
1.73-1.796.0010.08317.3554040.9950.09199.1
1.79-1.866.3070.07220.3151990.9960.07999.5
1.86-1.946.2220.06622.4749870.9970.07299.4
1.94-2.026.0740.06124.5248250.9970.06699.5
2.02-2.125.860.05626.4745910.9970.06299.4
2.12-2.246.5610.05529.7143610.9970.05999.3
2.24-2.376.5860.05131.4641460.9980.05699.3
2.37-2.546.540.0532.6539080.9970.05499.8
2.54-2.746.1930.04632.8936420.9980.05199.7
2.74-36.7120.04635.4233400.9980.0599.9
3-3.356.6410.04436.6230470.9980.04899.7
3.35-3.876.1870.04136.326780.9980.04599.6
3.87-4.746.6150.03838.1722820.9990.04199.8
4.74-6.716.580.03737.7417640.9990.0499.4
6.71-41.0456.5080.03438.039860.9990.03799.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1o98

1o98


Resolution: 1.5→41.045 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 15.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.164 2000 2.37 %
Rwork0.1349 --
obs0.1355 84298 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→41.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3895 0 49 700 4644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064132
X-RAY DIFFRACTIONf_angle_d1.1085601
X-RAY DIFFRACTIONf_dihedral_angle_d11.8121550
X-RAY DIFFRACTIONf_chiral_restr0.076625
X-RAY DIFFRACTIONf_plane_restr0.005741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.17341440.1445647X-RAY DIFFRACTION95
1.5375-1.57910.16871390.1345815X-RAY DIFFRACTION99
1.5791-1.62550.16691350.13565838X-RAY DIFFRACTION99
1.6255-1.6780.15961380.13815869X-RAY DIFFRACTION99
1.678-1.7380.17911430.14135843X-RAY DIFFRACTION99
1.738-1.80760.15751560.13825869X-RAY DIFFRACTION99
1.8076-1.88980.16841650.13675865X-RAY DIFFRACTION99
1.8898-1.98950.17291320.13645896X-RAY DIFFRACTION99
1.9895-2.11410.19031400.13955906X-RAY DIFFRACTION99
2.1141-2.27730.1471250.13995917X-RAY DIFFRACTION99
2.2773-2.50650.15861630.13945893X-RAY DIFFRACTION100
2.5065-2.86910.19231350.14335972X-RAY DIFFRACTION100
2.8691-3.61440.15421380.13115946X-RAY DIFFRACTION100
3.6144-41.06040.15141470.12286022X-RAY DIFFRACTION100
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)
10.2297-0.01990.09561.2906-0.19811.3809-0.01560.0223-0.0028-0.11620.0048-0.08030.01520.14110.00250.10840.0010.02160.11280.00260.10628.7741-7.5787.4233
20.03390.05560.41780.7221.05391.8846-0.05520.05610.0285-0.11040.05240.0203-0.09420.1588-0.02010.1225-0.01920.0090.13510.0080.13111.399717.149825.1481
30.50140.2790.01941.51910.56430.94530.0119-0.03920.01280.1211-0.0610.08090.0727-0.06280.03360.0694-0.00330.01630.0744-0.00790.07793.5346.669138.2623
41.68810.83612.79030.33031.22774.5461-0.16430.09240.0625-0.14190.05960.0161-0.41170.13770.14690.18830.0018-0.01540.08880.02210.13020.82616.94988.9082
50.34660.17450.01031.5516-1.18491.8051-0.0138-0.02120.04430.09430.04310.1344-0.2002-0.0736-0.03180.12780.01350.0060.12260.00580.1334-6.27741.762315.3256
60.6059-0.17170.47010.9091-0.41851.465-0.02250.0521-0.0123-0.09410.01780.0410.02880.0108-00.1003-0.00350.0090.0835-0.00390.09861.3085-8.156510.0455
71.0720.02420.35461.18590.67952.9711-0.02980.11980.0384-0.2524-0.0553-0.0887-0.02670.14560.08530.1768-0.02360.02670.12710.02060.1028.74084.9745-4.1229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 312 )
4X-RAY DIFFRACTION4chain 'A' and (resid 313 through 335 )
5X-RAY DIFFRACTION5chain 'A' and (resid 336 through 383 )
6X-RAY DIFFRACTION6chain 'A' and (resid 384 through 481 )
7X-RAY DIFFRACTION7chain 'A' and (resid 482 through 522 )

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