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- PDB-3b9t: Crystal structure of predicted acetamidase/formamidase (YP_546212... -

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Basic information

Entry
Database: PDB / ID: 3b9t
TitleCrystal structure of predicted acetamidase/formamidase (YP_546212.1) from Methylobacillus flagellatus KT at 1.58 A resolution
ComponentsTwin-arginine translocation pathway signal protein
KeywordsHYDROLASE / YP_546212.1 / predicted acetamidase/formamidase / Acetamidase/Formamidase family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyAcetamidase/Formamidase / Acetamidase/Formamidase family / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / metal ion binding / Twin-arginine translocation pathway signal
Function and homology information
Biological speciesMethylobacillus flagellatus KT (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of predicted acetamidase/formamidase (YP_546212.1) from Methylobacillus flagellatus KT at 1.58 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.5Nov 20, 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
Remark 999 SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 1. 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. 2. A PUTATIVE TWIN ARGININE SIGNAL PEPTIDE CLEAVAGE SITE IS LOCATED BETWEEN RESIDUES 57 AND 58. MASS SPECTROMETRY INDICATED THAT THE FULL LENGTH PROTEIN WAS PRESENT DURING PURIFICATION, HOWEVER, IT IS POSSIBLE THAT THE SHORTER CLEAVED PRODUCT WAS CRYSTALLIZED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Twin-arginine translocation pathway signal protein
B: Twin-arginine translocation pathway signal protein
C: Twin-arginine translocation pathway signal protein
D: Twin-arginine translocation pathway signal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,04655
Polymers214,2364
Non-polymers2,81051
Water30,5531696
1
A: Twin-arginine translocation pathway signal protein
B: Twin-arginine translocation pathway signal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,36825
Polymers107,1182
Non-polymers1,25023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
MethodPISA
2
C: Twin-arginine translocation pathway signal protein
D: Twin-arginine translocation pathway signal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,67830
Polymers107,1182
Non-polymers1,56028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.165, 82.723, 83.576
Angle α, β, γ (deg.)107.820, 105.810, 95.180
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 5 / Auth seq-ID: 69 - 480 / Label seq-ID: 70 - 481

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Twin-arginine translocation pathway signal protein


Mass: 53558.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacillus flagellatus KT (bacteria)
Species: Methylobacillus flagellatus / Strain: KT, DSM 6875 / Gene: YP_546212.1, Mfla_2104 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GZG6
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 62.068 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1696 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsREMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 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: 1.8 Å3/Da / Density % sol: 31.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: NANODROP, 1.0M LiCl, 20.0% PEG 6000, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2007 / Details: KOHZU: Double crystal Si(111)
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.58→29.814 Å / Num. obs: 196551 / % possible obs: 95.8 % / Redundancy: 1.9 % / Biso Wilson estimate: 13.67 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.58-1.621.90.4591.627870143340.45994.2
1.62-1.671.90.384227156139600.38494.4
1.67-1.711.90.3232.326465136070.32394.6
1.71-1.771.90.2722.825933133340.27295
1.77-1.821.90.2173.525047129100.21795.2
1.82-1.891.90.1774.124179124710.17795.3
1.89-1.961.90.1464.923392120760.14695.6
1.96-2.041.90.122622588116820.12295.8
2.04-2.131.90.1036.921586111980.10396.1
2.13-2.231.90.0937.420703107440.09396.2
2.23-2.361.90.0897.719581102200.08996.4
2.36-2.51.90.0877.81846096740.08796.5
2.5-2.671.90.0837.91739191080.08396.6
2.67-2.881.90.0788.31613484650.07896.3
2.88-3.161.90.0679.51453077740.06796.5
3.16-3.531.80.058111276470390.05896.6
3.53-4.081.80.052121089161960.05296.1
4.08-520.052121063453420.05298.7
5-7.0720.079.2833941820.0799
7.07-29.81420.0748.4443622350.07497.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.58→29.814 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.099 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.082
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. EDO, CL MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 5. MG IONS ARE MODELED BASED ON DENSITY AND COORDINATION. THE ASSIGNMENT OF MG AND THE EDO NEXT TO IT IS TENTATIVE. 6. THERE ARE NO DENSITIES FOR THE N-TERMINAL RESIDUES 0-63 OF A/C/D CHAINS AND 0-67 OF B CHAIN ALTHOUGH MASS SPECTROSCOPY INDICATED THAT THEY ARE LIKELY TO BE PRESENT DURING PURIFICATION. THE SEQUENCE ANALYSIS INDICATED THAT THIS PROTEIN LIKELY CONTAINS A TWIN ARGININE SIGNAL PEPTIDE WITH A PUTATIVE CLEAVAGE SITE BETWEEN RESIDUES 57 AND 58. AS A RESULT, IT IS ALSO POSSIBLE THAT THE SHORTER CLEAVED PRODUCT WAS CRYSTALLIZED. 7. RAMACHANDRAN OUTLIERS 349 FOR ALL CHAINS ARE SUPPORTED BY WELL DEFINED DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.177 9907 5 %RANDOM
Rwork0.138 ---
obs0.14 196547 95.77 %-
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: 13.157 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.25 Å20.34 Å2
2--0.37 Å2-0.12 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.58→29.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12906 0 174 1696 14776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02213635
X-RAY DIFFRACTIONr_bond_other_d0.0020.029295
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9518518
X-RAY DIFFRACTIONr_angle_other_deg0.929322687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46451753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.97224.133600
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.291152144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0831562
X-RAY DIFFRACTIONr_chiral_restr0.0950.21980
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022759
X-RAY DIFFRACTIONr_nbd_refined0.220.22537
X-RAY DIFFRACTIONr_nbd_other0.2040.210012
X-RAY DIFFRACTIONr_nbtor_refined0.1790.26590
X-RAY DIFFRACTIONr_nbtor_other0.0870.26881
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.21291
X-RAY DIFFRACTIONr_metal_ion_refined0.1740.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.238
X-RAY DIFFRACTIONr_mcbond_it1.82438940
X-RAY DIFFRACTIONr_mcbond_other0.73633448
X-RAY DIFFRACTIONr_mcangle_it2.296513607
X-RAY DIFFRACTIONr_scbond_it4.0185808
X-RAY DIFFRACTIONr_scangle_it5.052114866
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2357MEDIUM POSITIONAL0.120.5
2B2357MEDIUM POSITIONAL0.180.5
3C2357MEDIUM POSITIONAL0.10.5
4D2357MEDIUM POSITIONAL0.090.5
1A2748LOOSE POSITIONAL0.185
2B2748LOOSE POSITIONAL0.255
3C2748LOOSE POSITIONAL0.35
4D2748LOOSE POSITIONAL0.185
1A2357MEDIUM THERMAL1.252
2B2357MEDIUM THERMAL0.922
3C2357MEDIUM THERMAL1.32
4D2357MEDIUM THERMAL0.882
1A2748LOOSE THERMAL1.8510
2B2748LOOSE THERMAL1.5510
3C2748LOOSE THERMAL1.9410
4D2748LOOSE THERMAL1.4210
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 705 -
Rwork0.214 13595 -
all-14300 -
obs--94.25 %
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)
10.3478-0.06270.00890.21580.0950.4993-0.0612-0.0365-0.08370.0653-0.01720.01320.1640.04310.07840.03370.01820.0363-0.05170.0264-0.00319.079837.123711.9073
20.3407-0.06720.02850.3018-0.05010.2955-0.02280.0771-0.0219-0.0699-0.03390.0070.0606-0.01140.0568-0.0041-0.00660.0082-0.0068-0.0362-0.03028.020747.1373-22.2396
30.3452-0.0132-0.09750.1987-0.05350.2219-0.0075-0.03990.00110.0352-0.01120.0017-0.00750.0150.0187-0.0315-0.0031-0.0173-0.0276-0.0109-0.02877.223971.97121.7988
40.3551-0.0142-0.09180.1410.03480.28260.01450.0680.0595-0.0237-0.0208-0.0107-0.0332-0.00330.0063-0.03280.0068-0.0145-0.02270.025-0.012320.96882.0128-11.5192
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA64 - 48265 - 483
2X-RAY DIFFRACTION2BB68 - 48169 - 482
3X-RAY DIFFRACTION3CC64 - 48265 - 483
4X-RAY DIFFRACTION4DD68 - 48169 - 482

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