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- PDB-3rhd: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase Gap... -

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Basic information

Entry
Database: PDB / ID: 3rhd
TitleCrystal structure of glyceraldehyde-3-phosphate dehydrogenase GapN from Methanocaldococcus jannaschii DSM 2661 complexed with NADP
ComponentsLactaldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGRC / dehydrogenase / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


lactaldehyde dehydrogenase / lactaldehyde dehydrogenase (NAD+) activity
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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal ...: / : / 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Lactaldehyde dehydrogenase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 glyceraldehyde-3-phosphate dehydrogenase GapN from Methanocaldococcus jannaschii DSM 2661 complexed with NADP
Authors: Malashkevich, V.N. / Toro, R. / Seidel, R. / Garrett, S. / Foti, R. / Almo, S.C.
History
DepositionApr 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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

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Assembly

Deposited unit
A: Lactaldehyde dehydrogenase
B: Lactaldehyde dehydrogenase
C: Lactaldehyde dehydrogenase
D: Lactaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,4808
Polymers216,5064
Non-polymers2,9744
Water10,989610
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18750 Å2
ΔGint-54 kcal/mol
Surface area61210 Å2
MethodPISA
2
A: Lactaldehyde dehydrogenase
B: Lactaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7404
Polymers108,2532
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-17 kcal/mol
Surface area33990 Å2
MethodPISA
3
C: Lactaldehyde dehydrogenase
D: Lactaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7404
Polymers108,2532
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-18 kcal/mol
Surface area34130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.243, 77.384, 167.389
Angle α, β, γ (deg.)90.00, 118.29, 90.00
Int Tables number5
Space group name H-MC121
Detailsdimer

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Components

#1: Protein
Lactaldehyde dehydrogenase


Mass: 54126.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: 15669601, MJ1411 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q58806, lactaldehyde dehydrogenase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 35% MPD, 0.1M acetate, 4.5, 2 mM NADPH, 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: Feb 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 93993 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.116 / Χ2: 1.333 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.2-2.24545470.919196.5
2.24-2.285.346530.946198.6
2.28-2.325.446120.974199.60.918
2.32-2.375.546780.969199.90.827
2.37-2.425.647250.98811000.736
2.42-2.485.646371.03111000.655
2.48-2.545.647241.01111000.555
2.54-2.615.646711.04811000.434
2.61-2.695.647141.07111000.392
2.69-2.775.646801.08911000.341
2.77-2.875.646981.1311000.263
2.87-2.995.547181.18811000.221
2.99-3.125.546921.28711000.167
3.12-3.295.547071.394199.90.129
3.29-3.495.447181.53411000.104
3.49-3.765.347131.73111000.082
3.76-4.145.247141.954199.90.069
4.14-4.745.247472.168199.90.058
4.74-5.97547792.159199.90.059
5.97-504.948662.307199.80.049

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.49 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.28 Å
Translation2.5 Å45.28 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PQA

3pqa


Resolution: 2.2→19.96 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2117 / WRfactor Rwork: 0.1599 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8343 / SU B: 14.891 / SU ML: 0.167 / SU R Cruickshank DPI: 0.2902 / SU Rfree: 0.2197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 4688 5 %RANDOM
Rwork0.1794 ---
obs0.1823 93586 99.59 %-
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: 68.96 Å2 / Biso mean: 27.9527 Å2 / Biso min: 9.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14132 0 124 610 14866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02214663
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.99519852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07851874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07825.632593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.649152809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.351558
X-RAY DIFFRACTIONr_chiral_restr0.0830.22319
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110620
X-RAY DIFFRACTIONr_mcbond_it0.7023.59149
X-RAY DIFFRACTIONr_mcangle_it3.3755014882
X-RAY DIFFRACTIONr_scbond_it8.449505514
X-RAY DIFFRACTIONr_scangle_it0.8294.54943
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 310 -
Rwork0.261 6342 -
all-6652 -
obs--97.11 %
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)
10.6281-0.0348-0.11810.4174-0.05950.67670.03640.0650.14170.024-0.04130.1358-0.0496-0.13260.00490.0264-0.0036-0.00730.0711-0.03460.15993.4079-17.164123.7293
20.912-0.0623-0.28250.49730.13670.6602-0.03750.1119-0.0636-0.0098-0.0390.06380.1538-0.05770.07640.0812-0.0294-0.00580.0463-0.02410.046222.2864-47.995914.6322
30.97560.1563-0.09760.59960.03680.67040.0508-0.13170.19170.1479-0.0614-0.0615-0.09940.12060.01060.1234-0.0725-0.05150.1104-0.03970.109642.5821-15.354645.9899
40.7017-0.10540.02670.6398-0.15060.74140.0269-0.2198-0.0120.2375-0.02560.03330.1684-0.0298-0.00130.2588-0.087-0.00360.1433-0.00970.012423.8281-44.661359.8232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 464
2X-RAY DIFFRACTION2B9 - 464
3X-RAY DIFFRACTION3C9 - 464
4X-RAY DIFFRACTION4D9 - 464

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