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- PDB-3prl: Crystal structure of NADP-dependent glyceraldehyde-3-phosphate de... -

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Basic information

Entry
Database: PDB / ID: 3prl
TitleCrystal structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Bacillus halodurans C-125
ComponentsNADP-dependent glyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / dehydrogenase / PSI-biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / nucleotide binding
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMalashkevich, V.N. / Toro, R. / Seidel, R. / Garrett, S. / Foti, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Bacillus halodurans C-125
Authors: Malashkevich, V.N. / Toro, R. / Seidel, R. / Garrett, S. / Foti, R. / Almo, S.C.
History
DepositionNov 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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 / _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: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
B: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
C: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
D: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,6448
Polymers218,2604
Non-polymers3844
Water9,962553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16710 Å2
ΔGint-130 kcal/mol
Surface area62140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.302, 131.430, 83.891
Angle α, β, γ (deg.)90.000, 102.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase


Mass: 54564.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BAB05956.1, BH2237, gapN / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: Q9KAQ0, glyceraldehyde-3-phosphate dehydrogenase (NADP+)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 123229 / % possible obs: 99.7 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.107 / Χ2: 1.049 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.034.90.68461501.01699.7
2.03-2.0750.75361440.96899.7
2.07-2.1150.57360960.97399.7
2.11-2.155.10.48461570.97699.6
2.15-2.25.10.43261350.98499.6
2.2-2.255.10.37461571.00499.8
2.25-2.315.10.35961291.00999.7
2.31-2.375.10.29361251.01399.5
2.37-2.445.10.27261441.00999.8
2.44-2.525.10.23761641.0299.8
2.52-2.615.10.20661211.0299.7
2.61-2.715.10.17361861.04499.7
2.71-2.845.10.15661431.07299.8
2.84-2.995.10.12461801.10899.7
2.99-3.175.20.161361.16699.7
3.17-3.425.30.08161671.19299.9
3.42-3.765.20.06661881.29199.9
3.76-4.315.50.05962011.148100
4.31-5.435.70.05762191.04999.9
5.43-505.60.04962870.91299.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.67 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.95 Å
Translation2.5 Å38.95 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUH

1euh


Resolution: 2→19.98 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.864 / WRfactor Rfree: 0.2896 / WRfactor Rwork: 0.2358 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7363 / SU B: 16.481 / SU ML: 0.208 / SU R Cruickshank DPI: 0.2592 / SU Rfree: 0.2235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3063 6163 5 %RANDOM
Rwork0.2482 ---
obs0.2512 122972 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 112.73 Å2 / Biso mean: 27.901 Å2 / Biso min: 5.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14339 0 20 553 14912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02214604
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.97919816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17351910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72625.196587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.602152573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1851584
X-RAY DIFFRACTIONr_chiral_restr0.0920.22347
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110800
X-RAY DIFFRACTIONr_mcbond_it0.68910.59462
X-RAY DIFFRACTIONr_mcangle_it1.5875015266
X-RAY DIFFRACTIONr_scbond_it2.673505142
X-RAY DIFFRACTIONr_scangle_it0.0934.54546
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 453 -
Rwork0.303 8289 -
all-8742 -
obs--96.49 %
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)
10.8514-0.3437-0.13510.440.22620.2099-0.0879-0.0799-0.04540.06390.08290.0430.067-0.02180.0050.06780.0093-0.00040.07090.02110.0115-35.844317.1993-6.3989
20.54770.05880.1010.48790.11140.2845-0.0448-0.00310.0941-0.04460.02740.0223-0.06160.00960.01740.0389-0.0011-0.00890.0019-0.00110.0336-0.342847.986-8.3006
30.47240.0041-0.25750.4142-0.02540.70260.01360.0601-0.0129-0.1015-0.0029-0.0457-0.01180.0786-0.01070.03520.00490.00810.07590.00730.01153.005127.3884-37.7953
40.7509-0.04450.3280.3759-0.20830.60360.06950.13160.0417-0.05690.02680.0982-0.022-0.0985-0.09630.06130.03770.00470.14080.0570.0448-41.822237.2459-35.122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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