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- PDB-3zlb: Crystal structure of phosphoglycerate kinase from Streptococcus p... -

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Basic information

Entry
Database: PDB / ID: 3zlb
TitleCrystal structure of phosphoglycerate kinase from Streptococcus pneumoniae
ComponentsPHOSPHOGLYCERATE KINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / positive regulation of plasminogen activation / angiostatin binding / positive regulation of fibrinolysis / cell wall / glycolytic process / protease binding / cell surface / ATP binding / cytoplasm
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Phosphoglycerate kinase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsBernardo-Garcia, N. / Hermoso, J.A.
CitationJournal: Thromb. Haemost. / Year: 2014
Title: Pneumococcal phosphoglycerate kinase interacts with plasminogen and its tissue activator.
Authors: Fulde, M. / Bernardo-Garcia, N. / Rohde, M. / Nachtigall, N. / Frank, R. / Preissner, K.T. / Klett, J. / Morreale, A. / Chhatwal, G.S. / Hermoso, J.A. / Bergmann, S.
History
DepositionJan 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Other
Category: citation / pdbx_database_proc / pdbx_database_status
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_conn.ptnr2_label_seq_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: PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,95710
Polymers41,9861
Non-polymers9729
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.347, 78.227, 59.033
Angle α, β, γ (deg.)90.00, 96.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHOSPHOGLYCERATE KINASE /


Mass: 41985.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: D39 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15(PREP4) / References: UniProt: Q04LZ5, phosphoglycerate kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growDetails: 30% PEG 4000, 0.2 M MGCL2, 0.1 M TRIS-HCL PH 8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.78→46.93 Å / Num. obs: 34968 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 16.92 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.4
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VPE

1vpe


Resolution: 1.78→46.937 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 18.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1921 1751 5 %
Rwork0.1452 --
obs0.1475 34945 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→46.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 59 404 3418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113067
X-RAY DIFFRACTIONf_angle_d1.2794154
X-RAY DIFFRACTIONf_dihedral_angle_d14.6381117
X-RAY DIFFRACTIONf_chiral_restr0.067474
X-RAY DIFFRACTIONf_plane_restr0.007531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.82820.34051240.24632542X-RAY DIFFRACTION100
1.8282-1.88190.23361390.20542527X-RAY DIFFRACTION100
1.8819-1.94270.22261280.18162537X-RAY DIFFRACTION100
1.9427-2.01210.24691370.16682557X-RAY DIFFRACTION100
2.0121-2.09270.1981520.15282524X-RAY DIFFRACTION100
2.0927-2.18790.20131400.14652544X-RAY DIFFRACTION100
2.1879-2.30330.19031200.13872553X-RAY DIFFRACTION100
2.3033-2.44760.19141450.14172543X-RAY DIFFRACTION100
2.4476-2.63650.19151190.13432554X-RAY DIFFRACTION100
2.6365-2.90180.1831390.13712574X-RAY DIFFRACTION100
2.9018-3.32160.19291360.13392544X-RAY DIFFRACTION100
3.3216-4.18450.14841310.11912586X-RAY DIFFRACTION100
4.1845-46.95320.1811410.14572609X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 24.0032 Å / Origin y: -12.9341 Å / Origin z: -12.4408 Å
111213212223313233
T0.076 Å2-0.0214 Å2-0.0177 Å2-0.0692 Å20.0123 Å2--0.0648 Å2
L0.8548 °2-0.5118 °2-0.5571 °2-0.6448 °20.4366 °2--0.5921 °2
S0.0211 Å °0.0076 Å °0.0041 Å °-0.0322 Å °-0.0227 Å °-0.003 Å °-0.0289 Å °-0.0009 Å °0.0042 Å °
Refinement TLS groupSelection details: ALL

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