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- PDB-4qax: Crystal structure of post-catalytic binary complex of Phosphoglyc... -

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Basic information

Entry
Database: PDB / ID: 4qax
TitleCrystal structure of post-catalytic binary complex of Phosphoglycerate mutase from Staphylococcus aureus
Components2,3-bisphosphoglycerate-independent phosphoglycerate mutase
KeywordsISOMERASE / 2 / 3-Bisphosphoglycerate independent Phosphoglycerate mutase. / Glycolysis and Gluconeogenesis / Cytosol
Function / homology
Function and homology information


phosphoglycerate mutase (2,3-diphosphoglycerate-independent) / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity / glucose catabolic process / glycolytic process / manganese ion binding / carbohydrate metabolic process / cytosol
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-PHOSPHOGLYCERIC ACID / : / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsRoychowdhury, A. / Kundu, A. / Bose, M. / Gujar, A. / Das, A.K.
CitationJournal: To be Published
Title: STRUCTURAL AND FUNCCTIONAL ANALYSIS of PHOSPHOGLYCERATE MUTASE from STAPHYLOCOCCUS AUREUS
Authors: Roychowdhury, A. / Kundu, A. / Bose, M. / Gujar, A. / Mukherjee, S. / Das, A.K.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,7574
Polymers57,4611
Non-polymers2963
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.802, 80.689, 89.254
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 57460.805 Da / Num. of mol.: 1 / Fragment: UNP residues 3-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC 8325 / Gene: gpmI, SAOUHSC_00798 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q2G029, phosphoglycerate mutase (2,3-diphosphoglycerate-independent)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.28 Å3/Da / Density % sol: 46.08 % / Mosaicity: 0.24 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium chloride, 0.1M Bis Tris pH 6.5, 25%(w/v)Polyethyleneglycol 3350. , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 22, 2014 / Details: Varimax, osmic mirror
RadiationMonochromator: varimax, osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→59.855 Å / Num. all: 35850 / Num. obs: 35850 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.065 / Net I/σ(I): 22.6
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.115.70.3562.22874850110.1590.3565.196.7
2.11-2.247.10.253.13503149210.10.258.2100
2.24-2.397.20.1824.23312446210.0730.18211100
2.39-2.597.20.12963103443050.0510.12914.7100
2.59-2.837.20.0928.42900340020.0360.09219.4100
2.83-3.177.30.06212.32638436320.0240.06227.6100
3.17-3.667.20.04117.42327432120.0160.04140.6100
3.66-4.487.20.033201988527610.0130.03351.5100
4.48-6.347.10.02921.91546621650.0120.02952.8100
6.34-19.5266.70.02523.8820412200.010.02555.396.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation19.53 Å2.25 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREP11.0.05phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MY4

4my4


Resolution: 2→19.53 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.805 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1787 5 %RANDOM
Rwork0.1659 ---
obs0.1684 35796 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.19 Å2 / Biso mean: 24.117 Å2 / Biso min: 9.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-0 Å2
2--0.42 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 13 288 4235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194019
X-RAY DIFFRACTIONr_bond_other_d0.0010.023746
X-RAY DIFFRACTIONr_angle_refined_deg1.981.9565446
X-RAY DIFFRACTIONr_angle_other_deg1.01438617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9665502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16625.34206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73715673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2511519
X-RAY DIFFRACTIONr_chiral_restr0.170.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02914
LS refinement shellResolution: 2→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 129 -
Rwork0.215 2323 -
all-2452 -
obs--93.3 %
Refinement TLS params.Method: refined / Origin x: 20.1824 Å / Origin y: -10.9296 Å / Origin z: 6.2558 Å
111213212223313233
T0.0074 Å2-0.0015 Å2-0.0048 Å2-0.0459 Å20.0004 Å2--0.0085 Å2
L0.037 °20.0661 °2-0.0809 °2-0.3809 °2-0.1166 °2--0.1892 °2
S0.0055 Å °0.0028 Å °-0.0035 Å °0.0268 Å °-0.015 Å °0.0119 Å °-0.0162 Å °0.0104 Å °0.0095 Å °

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