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- PDB-2pc6: Crystal structure of putative acetolactate synthase- small subuni... -

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Basic information

Entry
Database: PDB / ID: 2pc6
TitleCrystal structure of putative acetolactate synthase- small subunit from Nitrosomonas europaea
ComponentsProbable acetolactate synthase isozyme III (Small subunit)
KeywordsLYASE / ACETOLACTATE SYNTHASE / REGULATORY SUBUNIT / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


acetolactate synthase regulator activity / acetolactate synthase activity / acetolactate synthase / valine biosynthetic process / isoleucine biosynthetic process / lyase activity / metal ion binding
Similarity search - Function
ACT domain / Acetolactate synthase, small subunit, C-terminal / Small subunit of acetolactate synthase / Acetolactate synthase, small subunit / AHAS, ACT domain / ACT-like. Chain A, domain 2 / Acetolactate synthase/Transcription factor NikR, C-terminal / ACT domain / ACT domain profile. / ACT domain ...ACT domain / Acetolactate synthase, small subunit, C-terminal / Small subunit of acetolactate synthase / Acetolactate synthase, small subunit / AHAS, ACT domain / ACT-like. Chain A, domain 2 / Acetolactate synthase/Transcription factor NikR, C-terminal / ACT domain / ACT domain profile. / ACT domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Acetolactate synthase
Similarity search - Component
Biological speciesNitrosomonas europaea ATCC 19718 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsPetkowski, J.J. / Chruszcz, M. / Zimmerman, M.D. / Zheng, H. / Cymborowski, M.T. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Edwards, A. / Minor, W. ...Petkowski, J.J. / Chruszcz, M. / Zimmerman, M.D. / Zheng, H. / Cymborowski, M.T. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Edwards, A. / Minor, W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2007
Title: Crystal structures of TM0549 and NE1324--two orthologs of E. coli AHAS isozyme III small regulatory subunit.
Authors: Petkowski, J.J. / Chruszcz, M. / Zimmerman, M.D. / Zheng, H. / Skarina, T. / Onopriyenko, O. / Cymborowski, M.T. / Koclega, K.D. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionMar 29, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionApr 10, 2007ID: 2FGD
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 1, 2012Group: Non-polymer description
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _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: Probable acetolactate synthase isozyme III (Small subunit)
B: Probable acetolactate synthase isozyme III (Small subunit)
C: Probable acetolactate synthase isozyme III (Small subunit)
D: Probable acetolactate synthase isozyme III (Small subunit)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,39510
Polymers74,2754
Non-polymers1206
Water3,603200
1
A: Probable acetolactate synthase isozyme III (Small subunit)
C: Probable acetolactate synthase isozyme III (Small subunit)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2185
Polymers37,1372
Non-polymers803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-40 kcal/mol
Surface area13840 Å2
MethodPISA, PQS
2
B: Probable acetolactate synthase isozyme III (Small subunit)
D: Probable acetolactate synthase isozyme III (Small subunit)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1775
Polymers37,1372
Non-polymers403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-27 kcal/mol
Surface area14130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.123, 122.123, 111.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: LEU / Refine code: 6 / Auth seq-ID: 1 - 163 / Label seq-ID: 3 - 165

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Probable acetolactate synthase isozyme III (Small subunit)


Mass: 18568.674 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea ATCC 19718 (bacteria)
Species: Nitrosomonas europaea / Strain: IFO 14298 / Gene: ilvH, NE1324 / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3) / References: UniProt: Q82UZ2, EC: 4.1.3.18
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 3 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2% TACSIMATE, 10% PEG 400, 0.1M KCl, 10mM CaCl2, 50 mM Na-HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2005 / Details: SI 111 CHANNEL
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→35.58 Å / Num. all: 28271 / Num. obs: 28271 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18.9 % / Biso Wilson estimate: 44.2 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 60.72
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 19.3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 7.35 / Rsym value: 0.431 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
SOLVERESOLVEphasing
Omodel building
Cootmodel building
CCP4model building
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-3000phasing
DMphasing
RESOLVEphasing
CCP4phasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.5→35.58 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 19.795 / SU ML: 0.226 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.427 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27573 1465 4.9 %RANDOM
Rwork0.20503 ---
all0.20846 28270 --
obs0.20846 28270 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.511 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2--1.08 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 27 200 5085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224987
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.83826737
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0555662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87424.082196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.98215896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3051544
X-RAY DIFFRACTIONr_chiral_restr0.1150.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023628
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.22310
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.23490
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0250.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5321.53345
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38125232
X-RAY DIFFRACTIONr_scbond_it3.0731782
X-RAY DIFFRACTIONr_scangle_it4.5384.51505
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1094 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.525
2Bloose positional0.615
3Cloose positional0.735
4Dloose positional0.675
1Aloose thermal3.0410
2Bloose thermal3.7410
3Cloose thermal2.7710
4Dloose thermal5.4410
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 108 -
Rwork0.265 2044 -
obs--100 %
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)
113.9844-10.64920.368824.5151-5.68818.0202-0.5562-0.0477-1.10661.18970.28880.81270.67710.01790.2674-0.3135-0.1140.08750.034-0.1015-0.022-0.944417.742610.018
23.53371.2367-2.79530.6616-0.74994.2042-0.12740.1929-0.0897-0.08120.10610.32870.0359-0.41270.0213-0.25450.00480.0531-0.0257-0.0692-0.1119-3.530621.080513.6925
32.9812-1.69660.29051.39351.02384.84970.048-0.4987-0.18990.0644-0.06490.03540.33730.11890.0169-0.1358-0.0798-0.0119-0.05790.0365-0.168126.086419.680916.5307
47.76852.46432.8621.2806-0.277422.41920.26240.2282-0.10250.32970.09720.92750.1623-0.5051-0.3597-0.2029-0.0527-0.0363-0.0296-0.0183-0.09860.580326.17051.5018
55.8484-0.43011.34426.439-2.54731.2446-0.3217-0.07350.44390.33870.23070.1148-0.9695-0.38030.0910.19540.1536-0.0805-0.11540.059-0.223213.8448-1.280734.2094
61.00240.10650.05040.74780.50861.46940.0478-0.25420.29120.0735-0.0632-0.0918-0.449-0.09650.0153-0.07590.0419-0.0219-0.1181-0.0172-0.118230.9153-11.449855.4229
713.9483-0.134-4.03582.96141.13954.61940.0651-0.1078-0.05810.1931-0.144-0.1851-0.3304-0.07530.0789-0.07110.0293-0.0551-0.20190.0021-0.208132.9345-10.780554.3405
813.3653.94736.48462.01672.56323.953-0.2665-0.07330.5809-0.25770.02370.31-0.6556-0.31820.2428-0.01520.0925-0.0813-0.1270.0932-0.145120.4482-9.609944.2958
93.19894.04644.6866138.9704-29.785516.3950.8931-1.19010.11521.0205-1.23221.9466-1.003-1.4330.33910.00980.16020.14240.27360.16960.00539.625629.429328.0795
104.4761.371-0.89121.2481.68894.82560.1373-0.76180.10190.4122-0.19860.1713-0.3868-0.41650.0613-0.0341-0.00320.11440.1150.0143-0.07777.0726.325228.4644
112.74221.78150.96184.1522-0.50943.59410.158-0.07170.33570.0013-0.16010.2643-0.1671-0.25010.0021-0.23070.0236-0.0175-0.0698-0.0319-0.124110.4536.14081.1153
128.5515-1.8341.67727.021-4.363919.8558-0.0583-1.5983-0.11220.50910.2443-0.21610.682-0.3642-0.186-0.0996-0.0017-0.00920.2257-0.0488-0.21220.633225.492328.021
139.72690.1879-2.83566.4579-4.91894.4924-0.44740.43292.2797-0.11730.5938-0.40770.8193-0.6264-0.14640.774-0.0316-0.31410.07750.21290.661129.29992.190134.3494
149.16022.71793.17394.6497-0.6115.1129-0.83620.99951.7324-1.4708-0.00250.2733-0.84060.73250.83880.4017-0.1229-0.1574-0.09540.20320.240837.4003-1.313834.4
153.0092-1.0652-0.01272.88910.53092.2998-0.0187-0.01380.0781-0.07280.14560.01030.09090.0812-0.127-0.13110.0792-0.0772-0.09750.0105-0.17619.9-25.042138.7166
1615.2858-3.56934.78255.77023.04655.0073-0.37440.27870.4924-0.76110.5639-0.3185-1.0450.1652-0.18950.0695-0.1389-0.0195-0.11720.1537-0.094440.4924-4.06544.1004
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 92 - 11
2X-RAY DIFFRACTION2AA10 - 8512 - 87
3X-RAY DIFFRACTION3AA86 - 14988 - 151
4X-RAY DIFFRACTION4AA150 - 163152 - 165
5X-RAY DIFFRACTION5BB2 - 784 - 80
6X-RAY DIFFRACTION6BB79 - 10881 - 110
7X-RAY DIFFRACTION7BB109 - 139111 - 141
8X-RAY DIFFRACTION8BB140 - 163142 - 165
9X-RAY DIFFRACTION9CC2 - 94 - 11
10X-RAY DIFFRACTION10CC10 - 8712 - 89
11X-RAY DIFFRACTION11CC88 - 15090 - 152
12X-RAY DIFFRACTION12CC151 - 163153 - 165
13X-RAY DIFFRACTION13DD4 - 416 - 43
14X-RAY DIFFRACTION14DD42 - 8544 - 87
15X-RAY DIFFRACTION15DD86 - 14988 - 151
16X-RAY DIFFRACTION16DD150 - 163152 - 165

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