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- PDB-3qfe: Crystal structures of a putative dihydrodipicolinate synthase fam... -

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Basic information

Entry
Database: PDB / ID: 3qfe
TitleCrystal structures of a putative dihydrodipicolinate synthase family protein from Coccidioides immitis
ComponentsPutative dihydrodipicolinate synthase family protein
KeywordsLYASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Coccidioides / Valley Fever / Coccidioidomycosis / pathogenic fungus / soil-born pathogen / putative uncharacterized protein
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structures of a putative dihydrodipicolinate synthase family protein from Coccidioides immitis
Authors: Edwards, T.E. / Gardberg, A.S. / Sankaran, B. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJan 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Putative dihydrodipicolinate synthase family protein
B: Putative dihydrodipicolinate synthase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,57012
Polymers67,1532
Non-polymers41710
Water3,369187
1
A: Putative dihydrodipicolinate synthase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7235
Polymers33,5771
Non-polymers1464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative dihydrodipicolinate synthase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8477
Polymers33,5771
Non-polymers2716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.760, 89.760, 371.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-317-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 6 / Auth seq-ID: 1 - 313 / Label seq-ID: 5 - 317

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Putative dihydrodipicolinate synthase family protein


Mass: 33576.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (fungus) / Strain: RS / Gene: CIMG_00151 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: CoimA.00447.a.A1 PW28367 at 24.64 mg/mL against CSHT screen condition B2, 0.2 M CaCl2, 0.1 M Na Hepes pH 7.5, 28% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 38337 / Num. obs: 38200 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 19.7 % / Biso Wilson estimate: 46.203 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 27.2
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.35-2.4117.80.5135.674882627492749100
2.41-2.480.4856.33487442689100
2.48-2.550.4716.89475062639100
2.55-2.630.368.54473812538100
2.63-2.710.3429.83453972462100
2.71-2.810.25212.24465582406100
2.81-2.910.18916.1455902309100
2.91-3.030.16118.83446752236100
3.03-3.170.13722.21438792159100
3.17-3.320.10927.95419212072100
3.32-3.50.09135.4389171964100
3.5-3.720.07540.9336666188399.4
3.72-3.970.06446.2934415174799.4
3.97-4.290.05653.61354561677100
4.29-4.70.04860.57331091542100
4.7-5.250.04958.94307491408100
5.25-6.070.05256.37277861267100
6.07-7.430.04761.57254101102100
7.43-10.510.03572.2919253882100
10.510.03466.48902746980.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 58.05 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.87 Å
Translation3 Å19.87 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v8z

2v8z


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2213 / WRfactor Rwork: 0.1901 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8642 / SU B: 12.502 / SU ML: 0.136 / SU R Cruickshank DPI: 0.2443 / SU Rfree: 0.2002 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 1902 5 %RANDOM
Rwork0.1993 ---
obs0.201 38011 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.46 Å2 / Biso mean: 40.6171 Å2 / Biso min: 12.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å21.17 Å20 Å2
2--2.34 Å20 Å2
3----3.51 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4393 0 16 187 4596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224512
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9786168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9725605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19523.397156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.715639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6851525
X-RAY DIFFRACTIONr_chiral_restr0.0850.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0223420
X-RAY DIFFRACTIONr_mcbond_it0.7481.53041
X-RAY DIFFRACTIONr_mcangle_it1.424852
X-RAY DIFFRACTIONr_scbond_it2.04131471
X-RAY DIFFRACTIONr_scangle_it3.3724.51313
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2130 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.365
LOOSE THERMAL2.8610
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 144 -
Rwork0.227 2585 -
all-2729 -
obs--99.38 %
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)
10.9869-0.3350.73820.8645-0.28822.75340.00230.02310.1443-0.0404-0.0739-0.0824-0.33570.28330.07160.0886-0.0840.00510.10280.00850.043214.3277-38.1394-12.9132
21.1175-0.6958-0.13471.64560.1481.85610.01830.0237-0.0085-0.0271-0.12220.1165-0.09-0.05110.10390.0197-0.006-0.00070.0268-0.02890.035442.4806-15.672-15.0522
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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