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- PDB-3c0b: Crystal structure of the conserved archaeal protein Q6M145. North... -

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Basic information

Entry
Database: PDB / ID: 3c0b
TitleCrystal structure of the conserved archaeal protein Q6M145. Northeast Structural Genomics Consortium target MrR63
ComponentsConserved archaeal protein Q6M145
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / XRAY / MrR63 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


conserved archaeal protein q6m145 / 4-[[4-(2-aminoethyl)phenoxy]-methyl]-2-furanmethanamine-glutamate synthase / Hydantoinase A/oxoprolinase / Hydantoinase/oxoprolinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Conserved archaeal protein
Similarity search - Component
Biological speciesMethanococcus maripaludis S2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-ray structure of the conserved archaeal protein Q6M145.
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJan 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Oct 20, 2021Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved archaeal protein Q6M145
B: Conserved archaeal protein Q6M145
C: Conserved archaeal protein Q6M145
D: Conserved archaeal protein Q6M145
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,9006
Polymers148,8204
Non-polymers802
Water2,882160
1
A: Conserved archaeal protein Q6M145

B: Conserved archaeal protein Q6M145
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4503
Polymers74,4102
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area2770 Å2
MethodPISA
2
C: Conserved archaeal protein Q6M145
D: Conserved archaeal protein Q6M145
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4503
Polymers74,4102
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.400, 87.266, 123.988
Angle α, β, γ (deg.)90.00, 110.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Conserved archaeal protein Q6M145


Mass: 37204.984 Da / Num. of mol.: 4
Mutation: K48N, I50V, D93N, G101S, Y106N, D146E, L182S, N187D, T254N, K268E, K269N, I284L, G294A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis S2 (archaea) / Species: Methanococcus maripaludis / Strain: S2 / LL / Gene: MMP0072 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6M145
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.15
Details: 25% PEG 400, 0.1M Calcium acetate, 0.1M MES, pH 6.15, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 121560 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.3
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.81 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 130737.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The Friedel pairs were used in phasing. BULK SOLVENT MODEL USED IN REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2594 5442 5 %RANDOM
Rwork0.2141 ---
obs0.2141 109470 90.6 %-
all-115947 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.2874 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 41.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.912 Å20 Å2-7.436 Å2
2---3.179 Å20 Å2
3----2.733 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9752 0 2 160 9914
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 778 4.9 %
Rwork0.23 15076 -
obs--78.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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