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- PDB-5m6d: Streptococcus pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 5m6d
TitleStreptococcus pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (SpGAPDH) crystal structure
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GAPDH / host/pathogen / plasminogen binding
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glucose metabolic process / NAD binding / NADP binding / metal ion binding
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGaboriaud, C. / Moreau, C.P. / Di Guilmi, A.M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INSB-05-02 France
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Deciphering Key Residues Involved in the Virulence-promoting Interactions between Streptococcus pneumoniae and Human Plasminogen.
Authors: Moreau, C. / Terrasse, R. / Thielens, N.M. / Vernet, T. / Gaboriaud, C. / Di Guilmi, A.M.
History
DepositionOct 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.5Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,38810
Polymers76,8812
Non-polymers5078
Water4,288238
1
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,77620
Polymers153,7614
Non-polymers1,01516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area17300 Å2
ΔGint-163 kcal/mol
Surface area47630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.041, 130.237, 79.837
Angle α, β, γ (deg.)90.00, 119.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase


Mass: 38440.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The active site cystein is oxidized, this why there seems to be a mismatch between sequence and coordinates, but this is not the case
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: gapdh, gap, gapA, gapA_3, ERS003549_02320, ERS019166_02194, ERS019420_02001, ERS019499_02096, ERS020135_02122, ERS020141_02006, ERS020142_02114, ERS020143_02138, ERS020145_02042, ERS020146_ ...Gene: gapdh, gap, gapA, gapA_3, ERS003549_02320, ERS019166_02194, ERS019420_02001, ERS019499_02096, ERS020135_02122, ERS020141_02006, ERS020142_02114, ERS020143_02138, ERS020145_02042, ERS020146_02116, ERS020147_02108, ERS020151_01255, ERS020155_02130, ERS020157_02177, ERS020178_05802, ERS020520_01871, ERS020522_01677, ERS020523_02061, ERS020524_02058, ERS020526_04928, ERS020526_06565, ERS020527_02055, ERS020531_01991, ERS020539_02263, ERS020541_02011, ERS020726_03159, ERS020822_04318, ERS020831_02217, ERS020873_02164, ERS020881_02198, ERS021047_02054, ERS021354_07537, ERS021360_02109, ERS021447_07389, ERS022199_02215, ERS022232_07453, ERS096208_02293, ERS232497_02152, ERS367628_02144, ERS367811_01576, ERS394170_00349, ERS409165_02221, ERS409372_02114, ERS409444_01606, ERS455085_02183, ERS515225_02154, SpnNT_02067
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus-RIL
References: UniProt: I6L8L9, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 5 types, 246 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 12% PEG 6000, 0.1 M MgCl2, 0.1 M ADA, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 48531 / % possible obs: 99.6 % / Redundancy: 3.8 % / Net I/σ(I): 15.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LVF

3lvf


Resolution: 2→40.516 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.88
RfactorNum. reflection% reflection
Rfree0.2148 2466 5.1 %
Rwork0.1953 --
obs0.1963 48379 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→40.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5136 0 29 238 5403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055345
X-RAY DIFFRACTIONf_angle_d0.887258
X-RAY DIFFRACTIONf_dihedral_angle_d12.7753208
X-RAY DIFFRACTIONf_chiral_restr0.054840
X-RAY DIFFRACTIONf_plane_restr0.006953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03850.32661560.31092522X-RAY DIFFRACTION99
2.0385-2.08010.3521440.29492541X-RAY DIFFRACTION100
2.0801-2.12530.28461230.27022564X-RAY DIFFRACTION100
2.1253-2.17480.32181300.2692517X-RAY DIFFRACTION100
2.1748-2.22910.26221200.24282549X-RAY DIFFRACTION99
2.2291-2.28940.2431390.25342536X-RAY DIFFRACTION99
2.2894-2.35680.27851300.23362540X-RAY DIFFRACTION100
2.3568-2.43280.20471340.23062574X-RAY DIFFRACTION100
2.4328-2.51980.25751400.22422530X-RAY DIFFRACTION100
2.5198-2.62060.24241590.22362539X-RAY DIFFRACTION100
2.6206-2.73990.23321410.20872546X-RAY DIFFRACTION100
2.7399-2.88430.22591400.20852542X-RAY DIFFRACTION100
2.8843-3.0650.21941520.19912557X-RAY DIFFRACTION100
3.065-3.30150.22011330.19342539X-RAY DIFFRACTION100
3.3015-3.63360.21811230.18262583X-RAY DIFFRACTION100
3.6336-4.15890.17791530.16972548X-RAY DIFFRACTION100
4.1589-5.2380.17221200.14622575X-RAY DIFFRACTION100
5.238-100.17171290.16842611X-RAY DIFFRACTION99
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)
12.68392.39630.92083.70640.73322.0932-0.12110.0683-0.5065-0.24390.08950.14450.4954-0.19070.07420.4702-0.05880.12560.3744-0.15760.84247.24551.361122.4391
21.14970.1515-0.7061.3251.4855.5177-0.12540.2213-0.321-0.0543-0.12520.60790.1679-0.56080.21260.3602-0.03620.09510.3937-0.11130.9518-5.662756.977726.3002
33.63791.6487-1.69192.9068-0.62251.1073-0.35490.6007-0.5569-0.16620.07370.76370.1205-0.53550.20850.2084-0.00460.01920.3402-0.06550.48172.83677.350934.4121
41.78240.35180.01432.0520.13580.9837-0.2387-0.1841-0.84260.29110.00860.40220.2475-0.17890.21240.32960.01890.21290.31470.06150.67921.652965.079845.1114
52.356-0.7567-1.71432.41360.37022.30850.0874-1.5440.470.77810.119-0.4397-0.41121.1585-0.23620.6268-0.0937-0.09151.0019-0.15190.368126.120597.713756.7134
62.6337-1.1151-2.79852.87561.63582.7236-0.2408-1.0144-0.66140.87940.13520.28860.02760.44020.08530.38890.06230.09190.41590.13170.294216.374676.593552.0992
72.7077-0.1814-0.66252.27670.13361.5855-0.0231-0.4487-0.03690.50120.02090.4101-0.1348-0.02060.01820.32420.04890.07830.30150.02660.22865.66588.837650.2136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 186 )
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 219 )
4X-RAY DIFFRACTION4chain 'A' and (resid 220 through 355 )
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 186 )
6X-RAY DIFFRACTION6chain 'B' and (resid 187 through 219 )
7X-RAY DIFFRACTION7chain 'B' and (resid 220 through 355 )

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