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- PDB-3d4o: Crystal structure of dipicolinate synthase subunit A (NP_243269.1... -

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Basic information

Entry
Database: PDB / ID: 3d4o
TitleCrystal structure of dipicolinate synthase subunit A (NP_243269.1) from BACILLUS HALODURANS at 2.10 A resolution
ComponentsDipicolinate synthase subunit A
KeywordsOXIDOREDUCTASE / NP_243269.1 / dipicolinate synthase subunit A / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Alanine dehydrogenase/PNT / C-terminal domain COMPLEX
Function / homology
Function and homology information


Dipicolinic acid synthetase subunit A / Dipicolinate synthase subunit A, N-terminal / Dipicolinate synthase subunit A N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Dipicolinate synthase subunit A
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of dipicolinate synthase subunit A (NP_243269.1) from BACILLUS HALODURANS at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Oct 9, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dipicolinate synthase subunit A
B: Dipicolinate synthase subunit A
C: Dipicolinate synthase subunit A
D: Dipicolinate synthase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,50418
Polymers128,5474
Non-polymers95714
Water11,385632
1
A: Dipicolinate synthase subunit A
C: Dipicolinate synthase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7348
Polymers64,2732
Non-polymers4606
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-4 kcal/mol
Surface area24450 Å2
MethodPISA
2
B: Dipicolinate synthase subunit A
D: Dipicolinate synthase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,77010
Polymers64,2732
Non-polymers4978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint5.7 kcal/mol
Surface area24490 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
ΔGint-9 kcal/mol
Surface area45090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.650, 142.420, 74.860
Angle α, β, γ (deg.)90.000, 93.490, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / Refine code: 5

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA1 - 2912 - 292
21PROPROBB1 - 2912 - 292
12GLUGLUCC1 - 2902 - 291
22GLUGLUDD1 - 2902 - 291

NCS ensembles :
ID
1
2
DetailsAUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Dipicolinate synthase subunit A


Mass: 32136.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: NP_243269.1, spoVFA, BH2403 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9KA87
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 14.5% polyethylene glycol 3350, 0.279M di-sodium tartrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 17, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→29.775 Å / Num. obs: 72049 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.478 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 6.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.170.4581.9245711290596
2.17-2.260.3532.4282741470398.4
2.26-2.360.2683266641385098.4
2.36-2.490.2193.6287161486598.7
2.49-2.640.1754.4262241356398.4
2.64-2.850.1365.5283161460298.3
2.85-3.130.0917.4269921388198.4
3.13-3.590.05710.6279971435498.1
3.59-4.510.03714.8272291392497.9
4.510.03316.1275311403996.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→29.775 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.076 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.191
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TARTARATE (TAR) AND ETHYLENE GLYCOL (EDO) MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTIONS ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3729 5.2 %RANDOM
Rwork0.189 ---
obs0.192 72015 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.44 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å2-0.25 Å2
2--0.04 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8645 0 62 632 9339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228886
X-RAY DIFFRACTIONr_bond_other_d0.0030.025881
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.97912038
X-RAY DIFFRACTIONr_angle_other_deg1.533314493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.44851177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.1424.304316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.285151555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4941550
X-RAY DIFFRACTIONr_chiral_restr0.0880.21486
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219770
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021636
X-RAY DIFFRACTIONr_mcbond_it1.15725783
X-RAY DIFFRACTIONr_mcbond_other0.26522384
X-RAY DIFFRACTIONr_mcangle_it2.19949341
X-RAY DIFFRACTIONr_scbond_it4.21963103
X-RAY DIFFRACTIONr_scangle_it6.00982686
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1687MEDIUM POSITIONAL0.210.5
1A1838LOOSE POSITIONAL0.365
1A1687MEDIUM THERMAL0.662
1A1838LOOSE THERMAL0.7910
2C1699MEDIUM POSITIONAL0.170.5
2C1800LOOSE POSITIONAL0.465
2C1699MEDIUM THERMAL0.62
2C1800LOOSE THERMAL0.810
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.233 5213 -
obs--96.97 %
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)
11.2544-0.43630.40441.2488-0.31910.74090.06710.1990.1047-0.1886-0.00150.0495-0.05970.0213-0.0656-0.1228-0.02610.0126-0.110.0236-0.16028.97461.97633.959
21.34730.50770.44841.3540.10930.51550.0465-0.15960.13110.25630.0094-0.0437-0.072-0.0582-0.0559-0.10090.03040.014-0.1264-0.0185-0.16113.15762.0372.986
32.0955-0.2578-0.68820.82910.11631.0656-0.08840.2596-0.3875-0.11790.0074-0.07330.2682-0.00510.081-0.0257-0.04140.0045-0.1036-0.0786-0.04416.24925.39934.263
41.4470.4134-0.44191.1133-0.22981.42980.0083-0.1647-0.21270.1135-0.00370.04040.266-0.0928-0.0046-0.0633-0.0013-0.02-0.12660.0357-0.08355.31125.38872.794
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 391 - 40
2X-RAY DIFFRACTION1AA42 - 29143 - 292
3X-RAY DIFFRACTION2BB0 - 391 - 40
4X-RAY DIFFRACTION2BB41 - 29142 - 292
5X-RAY DIFFRACTION3CC0 - 2901 - 291
6X-RAY DIFFRACTION4DD0 - 391 - 40
7X-RAY DIFFRACTION4DD41 - 29042 - 291

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