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- PDB-4ng4: Structure of phosphoglycerate kinase (CBU_1782) from Coxiella burnetii -

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Basic information

Entry
Database: PDB / ID: 4ng4
TitleStructure of phosphoglycerate kinase (CBU_1782) from Coxiella burnetii
ComponentsPhosphoglycerate kinase
KeywordsTRANSFERASE / phosphoglycerate kinase
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / positive regulation of oxidative phosphorylation / ADP binding / gluconeogenesis / glycolytic process / ATP binding / cytosol
Similarity search - Function
Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Phosphoglycerate kinase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsFranklin, M.C. / Cheung, J. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionNov 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 20, 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_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_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_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_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Phosphoglycerate kinase
B: Phosphoglycerate kinase
C: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,6839
Polymers131,3293
Non-polymers1,3556
Water0
1
A: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2283
Polymers43,7761
Non-polymers4522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2283
Polymers43,7761
Non-polymers4522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2283
Polymers43,7761
Non-polymers4522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.148, 91.568, 88.412
Angle α, β, γ (deg.)90.00, 102.17, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A5 - 170
2112B5 - 170
3112C5 - 170
1122A171 - 396
2122B171 - 396
3122C171 - 396

NCS ensembles :
ID
1
2

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Components

#1: Protein Phosphoglycerate kinase /


Mass: 43776.285 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: This construct's boundaries were selected based on the GenBank gene sequence. However, the N terminus of the GenBank sequence was later discovered to be incorrect; based on homology to other ...Details: This construct's boundaries were selected based on the GenBank gene sequence. However, the N terminus of the GenBank sequence was later discovered to be incorrect; based on homology to other phosphoglycerate kinases, the correct N terminus is five residues later, i.e. MKALP... Residue numbering in this structure reflects the correct N terminus.
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 / Nine Mile phase I / Gene: CBU_1782, pgk / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83AU6, phosphoglycerate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Sequence detailsTHIS CONSTRUCT'S BOUNDARIES WERE SELECTED BASED ON THE GENBANK GENE SEQUENCE. HOWEVER, THE N ...THIS CONSTRUCT'S BOUNDARIES WERE SELECTED BASED ON THE GENBANK GENE SEQUENCE. HOWEVER, THE N TERMINUS OF THE GENBANK SEQUENCE WAS LATER DISCOVERED TO BE INCORRECT; BASED ON HOMOLOGY TO OTHER PHOSPHOGLYCERATE KINASES, THE CORRECT N TERMINUS IS FIVE RESIDUES LATER, I.E. MKALP... RESIDUE NUMBERING IN THIS STRUCTURE REFLECTS THE CORRECT N TERMINUS.

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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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sodium chloride, HEPES, PEG 3000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. all: 30881 / Num. obs: 30663 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.129 / Net I/σ(I): 11.3
Reflection shellResolution: 2.78→2.85 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1532 / Rsym value: 0.522 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology models of cbu_1782 sequence built on the coordinates of 1ZMR, split into two domains

1zmr


Resolution: 2.78→43.21 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.828 / SU B: 42.915 / SU ML: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31264 1538 5 %RANDOM
Rwork0.27231 ---
obs0.27432 29124 98.05 %-
all-31271 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.646 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å21.54 Å2
2---2.34 Å20 Å2
3---4.08 Å2
Refinement stepCycle: LAST / Resolution: 2.78→43.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8802 0 84 0 8886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229020
X-RAY DIFFRACTIONr_bond_other_d0.0010.026029
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.98212217
X-RAY DIFFRACTIONr_angle_other_deg0.845314856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1251153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.42325.647363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.373151597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5951538
X-RAY DIFFRACTIONr_chiral_restr0.0630.21433
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029927
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021640
X-RAY DIFFRACTIONr_mcbond_it0.1951.55764
X-RAY DIFFRACTIONr_mcbond_other0.061.52361
X-RAY DIFFRACTIONr_mcangle_it0.36429226
X-RAY DIFFRACTIONr_scbond_it0.73233256
X-RAY DIFFRACTIONr_scangle_it1.1224.52991
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A944TIGHT POSITIONAL0.020.05
12B944TIGHT POSITIONAL0.020.05
13C944TIGHT POSITIONAL0.020.05
11A1175MEDIUM POSITIONAL0.020.5
12B1175MEDIUM POSITIONAL0.020.5
13C1175MEDIUM POSITIONAL0.020.5
11A944TIGHT THERMAL0.040.5
12B944TIGHT THERMAL0.040.5
13C944TIGHT THERMAL0.040.5
11A1175MEDIUM THERMAL0.042
12B1175MEDIUM THERMAL0.042
13C1175MEDIUM THERMAL0.052
21A1307TIGHT POSITIONAL0.020.05
22B1307TIGHT POSITIONAL0.020.05
23C1307TIGHT POSITIONAL0.020.05
21A1431MEDIUM POSITIONAL0.020.5
22B1431MEDIUM POSITIONAL0.020.5
23C1431MEDIUM POSITIONAL0.020.5
21A1307TIGHT THERMAL0.040.5
22B1307TIGHT THERMAL0.040.5
23C1307TIGHT THERMAL0.040.5
21A1431MEDIUM THERMAL0.042
22B1431MEDIUM THERMAL0.052
23C1431MEDIUM THERMAL0.052
LS refinement shellResolution: 2.78→2.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 81 -
Rwork0.288 1804 -
obs--82.71 %
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)
15.0344-1.0373-1.40134.3206-0.39315.51420.54551.02890.8335-0.4593-0.374-0.0234-0.1955-0.0743-0.17150.09450.140.0780.30750.17680.1458-28.4943-1.116316.7304
22.3691-0.5925-0.10452.3378-1.00633.37990.22340.29310.328-0.0885-0.1609-0.0147-0.11010.0271-0.06250.02620.0290.02910.05080.01430.113-1.5977-18.052929.1392
34.38010.72080.23533.4071.61464.4216-0.28120.7026-0.4228-0.39580.3067-0.62030.15140.2409-0.02560.1697-0.14580.09370.2341-0.08750.1723-15.83344.303917.3766
43.11770.6657-1.12942.26250.31132.8638-0.2470.3503-0.2037-0.13230.2836-0.22630.09740.1415-0.03670.0373-0.0344-0.00150.0798-0.04440.0699-44.85330.366729.192
53.21910.47520.89764.4306-0.24985.6567-0.04840.2062-0.2195-0.80310.06090.50010.025-0.3664-0.01260.23870.0164-0.1020.052-0.01970.082316.149911.877717.3959
61.74520.0470.76932.31230.52892.32360.00080.0357-0.0513-0.31770.02090.21990.0046-0.1497-0.02180.0662-0.0038-0.0310.01890.01380.09218.370943.618529.0636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 170
2X-RAY DIFFRACTION2A171 - 394
3X-RAY DIFFRACTION3B5 - 170
4X-RAY DIFFRACTION4B171 - 394
5X-RAY DIFFRACTION5C5 - 170
6X-RAY DIFFRACTION6C171 - 396

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