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- PDB-6cib: The structure of YcaO from Methanopyrus kandleri bound with AMPPC... -

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Basic information

Entry
Database: PDB / ID: 6cib
TitleThe structure of YcaO from Methanopyrus kandleri bound with AMPPCP and Mg2+
ComponentsYcaO
KeywordsBIOSYNTHETIC PROTEIN / thioamidation / YcaO / ADP / Mg
Function / homologyPutative methanogenesis marker protein 1 / YcaO-like domain / YcaO cyclodehydratase, ATP-ad Mg2+-binding / YcaO domain profile. / nucleotide binding / metal ion binding / ADENOSINE-5'-DIPHOSPHATE / OXAMIC ACID / Uncharacterized conserved protein
Function and homology information
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsDong, S.-H. / Nair, S.K.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Enzymatic reconstitution of ribosomal peptide backbone thioamidation.
Authors: Mahanta, N. / Liu, A. / Dong, S. / Nair, S.K. / Mitchell, D.A.
History
DepositionFeb 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YcaO
B: YcaO
C: YcaO
D: YcaO
E: YcaO
F: YcaO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,57724
Polymers258,3346
Non-polymers3,24318
Water27,7071538
1
A: YcaO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5964
Polymers43,0561
Non-polymers5413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YcaO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5964
Polymers43,0561
Non-polymers5413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: YcaO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5964
Polymers43,0561
Non-polymers5413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: YcaO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5964
Polymers43,0561
Non-polymers5413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: YcaO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5964
Polymers43,0561
Non-polymers5413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: YcaO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5964
Polymers43,0561
Non-polymers5413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.232, 105.627, 139.298
Angle α, β, γ (deg.)90.00, 103.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
YcaO


Mass: 43055.613 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938) (archaea)
Strain: AV19 / DSM 6324 / JCM 9639 / NBRC 100938 / Gene: MK0115 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZ25
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1538 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.44 Å3/Da / Density % sol: 64.25 %
Crystal growTemperature: 282.1 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate (tribasic), 0.02 M sodium potassium tartrate, 0.02 M sodium oxamate, 0.05 M HEPES pH=7.5, 0.05 M MOPS pH=7.5, 20% glycerol, and 10% PEG 4000
Temp details: 9 C

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen flow
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07822 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07822 Å / Relative weight: 1
ReflectionResolution: 2.04→80.7 Å / Num. obs: 200362 / % possible obs: 90.8 % / Redundancy: 4.1 % / Net I/σ(I): 9.8
Reflection shellResolution: 2.05→2.103 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
SHARPphasing
RefinementResolution: 2.05→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.417 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23361 9774 5 %RANDOM
Rwork0.19459 ---
obs0.19652 187537 90.77 %-
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: 40.236 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å20.52 Å2
2--0.95 Å20 Å2
3---0.96 Å2
Refinement stepCycle: 1 / Resolution: 2.05→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17352 0 204 1538 19094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01917907
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.99424312
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5852157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47322.509881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.111152964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.61615240
X-RAY DIFFRACTIONr_chiral_restr0.0870.22675
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113722
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.73.7728670
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.835.63710813
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3834.1349237
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.19652.23527348
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 660 -
Rwork0.293 12693 -
obs--83.97 %

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