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- PDB-3cmn: Crystal structure of a putative hydrolase with a novel fold from ... -

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Basic information

Entry
Database: PDB / ID: 3cmn
TitleCrystal structure of a putative hydrolase with a novel fold from Chloroflexus aurantiacus
ComponentsPutative hydrolase
KeywordsHYDROLASE / PSI-II / NYSGXRC / Putative hydrolase / apoenzyme / helical protein / 10492m / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homologyZincin-like metallopeptidase, N-terminal domain / Zinicin-like metallopeptidase type 2 / Conserved hypothetical protein CHP03883, F420 biosynthesis associated / Zinicin-like metallopeptidase type 2, N-terminal / Zincin-like metallopeptidase / Lysin / Up-down Bundle / Mainly Alpha / Coenzyme F420 biosynthesis-associated protein
Function and homology information
Biological speciesChloroflexus aurantiacus J-10-fl (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative hydrolase with a novel fold from Chloroflexus aurantiacus.
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionMar 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative hydrolase


Theoretical massNumber of molelcules
Total (without water)42,6991
Polymers42,6991
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.968, 75.968, 124.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Putative hydrolase


Mass: 42698.551 Da / Num. of mol.: 1 / Fragment: Residues 30-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus J-10-fl (bacteria)
Species: Chloroflexus aurantiacus / Strain: J-10-fl / DSM 635 / Gene: Caur_0242 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: A9WCA2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1.5 M Sodium chloride, 10% Ethanol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 18, 2008
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 17996 / Num. obs: 17996 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 24.4 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.3
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1 / Num. unique all: 1693 / % possible all: 97.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→49.34 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 60793.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 489 2.9 %RANDOM
Rwork0.247 ---
obs0.247 16927 94 %-
all-17996 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.0922 Å2 / ksol: 0.371968 e/Å3
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.38 Å20 Å20 Å2
2--3.38 Å20 Å2
3----6.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.25→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 0 76 2515
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 72 2.9 %
Rwork0.325 2409 -
obs-17996 84.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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