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- PDB-2qj8: Crystal structure of an aspartoacylase family protein (mlr6093) f... -

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Basic information

Entry
Database: PDB / ID: 2qj8
TitleCrystal structure of an aspartoacylase family protein (mlr6093) from mesorhizobium loti maff303099 at 2.00 A resolution
ComponentsMlr6093 protein
KeywordsHYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologySuccinylglutamate desuccinylase/aspartoacylase / Succinylglutamate desuccinylase / Aspartoacylase family / hydrolase activity, acting on ester bonds / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Mlr6093 protein
Function and homology information
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein mlr6093 (NP_106651.1) from Mesorhizobium loti at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 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 1.5Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS WHICH FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mlr6093 protein
B: Mlr6093 protein


Theoretical massNumber of molelcules
Total (without water)72,0642
Polymers72,0642
Non-polymers00
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-15 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.054, 86.140, 94.632
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: SER / Refine code: 4

Dom-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ARGAA2 - 3313 - 332
2ALABB2 - 3303 - 331

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Components

#1: Protein Mlr6093 protein


Mass: 36032.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: NP_106651.1, mlr6093 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q98AA0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 20.0% PEG 3350, 0.2M Potassium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.978662 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 2007
Details: 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing
RadiationMonochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978662 Å / Relative weight: 1
ReflectionResolution: 2→29.643 Å / Num. obs: 45402 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 26.79 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.053.80.7821.71228532680.78298.7
2.05-2.114.60.7440.61502932410.744100
2.11-2.174.80.5531.41501831350.553100
2.17-2.244.70.4991.11423530610.499100
2.24-2.314.70.4311398529680.43100
2.31-2.394.80.3162.41370928640.316100
2.39-2.484.80.2671.91338227900.267100
2.48-2.584.80.2113.51276826700.211100
2.58-2.74.70.193.41209425840.19100
2.7-2.834.80.1415.21167924460.141100
2.83-2.984.80.1146.21120223540.114100
2.98-3.164.80.0927.51060522190.092100
3.16-3.384.70.0749996521220.074100
3.38-3.654.60.0688.2889719320.068100
3.65-44.60.05910832518270.059100
4-4.474.70.04812.6771316520.048100
4.47-5.164.60.05111.6674514640.051100
5.16-6.324.50.05810.3563612560.05899.8
6.32-8.944.30.04713.143209940.04799.6
8.94-29.6433.90.04413.421585550.04495.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.643 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.618 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.175
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. RESIDUES A210-A215, A238-A247, B26-B28, B91-B115, B156-B160, B183-B188 AND B213-B214 ARE DISORDERED AND HAVE NOT BEEN MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2286 5 %RANDOM
Rwork0.207 ---
obs0.209 45330 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.569 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20 Å2
2---0.25 Å20 Å2
3---1.82 Å2
Refinement stepCycle: LAST / Resolution: 2→29.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4499 0 0 282 4781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224779
X-RAY DIFFRACTIONr_bond_other_d0.0040.023227
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.9766544
X-RAY DIFFRACTIONr_angle_other_deg1.36737947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0035650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68323.596178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33615801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0751533
X-RAY DIFFRACTIONr_chiral_restr0.1030.2782
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025331
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02910
X-RAY DIFFRACTIONr_nbd_refined0.1650.3854
X-RAY DIFFRACTIONr_nbd_other0.1490.33335
X-RAY DIFFRACTIONr_nbtor_refined0.160.52238
X-RAY DIFFRACTIONr_nbtor_other0.0820.52507
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.5431
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0750.37
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1330.354
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.524
X-RAY DIFFRACTIONr_mcbond_it1.79233231
X-RAY DIFFRACTIONr_mcbond_other0.66331249
X-RAY DIFFRACTIONr_mcangle_it2.5355038
X-RAY DIFFRACTIONr_scbond_it4.34681795
X-RAY DIFFRACTIONr_scangle_it5.896111480
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3168 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.710.5
MEDIUM THERMAL1.382
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 168 -
Rwork0.283 3072 -
obs-3240 98.03 %
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)
11.584-0.58990.21171.15260.10860.066-0.02560.00710.10810.0290.00050.115-0.0454-0.0420.0251-0.0732-0.00670.0067-0.1095-0.0037-0.115475.175958.177718.9259
25.0263-0.3734-0.90710.03750.07130.16520.09040.079-0.43930.0279-0.0698-0.00170.05960.0138-0.02060.0106-0.0022-0.0471-0.0189-0.0156-0.023748.504237.873314.2727
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 3313 - 332
2X-RAY DIFFRACTION2BB1 - 3302 - 331

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