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- PDB-4q7q: The crystal structure of a possible lipase from Chitinophaga pine... -

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Basic information

Entry
Database: PDB / ID: 4q7q
TitleThe crystal structure of a possible lipase from Chitinophaga pinensis DSM 2588
ComponentsLipolytic protein G-D-S-L family
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / protein structure initiative / MCSG / Midwest Center for Structural Genomics
Function / homologySGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID / Lipolytic protein G-D-S-L family
Function and homology information
Biological speciesChitinophaga pinensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.451 Å
AuthorsTan, K. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a possible lipase from Chitinophaga pinensis DSM 2588
Authors: Tan, K. / Tesar, C. / Clancy, S. / Joachimiak, A.
History
DepositionApr 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 27, 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 / struct_conn / 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.pdbx_leaving_atom_flag / _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: Lipolytic protein G-D-S-L family
B: Lipolytic protein G-D-S-L family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4769
Polymers60,0272
Non-polymers4497
Water8,287460
1
A: Lipolytic protein G-D-S-L family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2894
Polymers30,0131
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipolytic protein G-D-S-L family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1875
Polymers30,0131
Non-polymers1744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.611, 80.611, 93.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Lipolytic protein G-D-S-L family


Mass: 30013.492 Da / Num. of mol.: 2 / Fragment: UNP residues 20-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chitinophaga pinensis (bacteria) / Strain: DSM 2588 / Gene: Cpin_6674 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: C7PNH7
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.1M CHES:NaOH, 30% (v/v) PEG 400, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2014 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.45→30.2 Å / Num. all: 104383 / Num. obs: 104383 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 9.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 46.3
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 3.6 / Num. unique all: 5192 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.451→30.2 Å / SU ML: 0.14 / σ(F): 1.39 / Phase error: 17.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 5213 5 %random
Rwork0.1532 ---
obs0.155 104334 99.63 %-
all-104334 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.451→30.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4089 0 27 460 4576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054238
X-RAY DIFFRACTIONf_angle_d0.9885768
X-RAY DIFFRACTIONf_dihedral_angle_d12.1811540
X-RAY DIFFRACTIONf_chiral_restr0.071624
X-RAY DIFFRACTIONf_plane_restr0.005753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.451-1.46780.24821510.1813046X-RAY DIFFRACTION92
1.4678-1.48510.24451970.1743264X-RAY DIFFRACTION100
1.4851-1.50320.20721730.15823348X-RAY DIFFRACTION100
1.5032-1.52220.23261600.14953298X-RAY DIFFRACTION100
1.5222-1.54220.19221610.1423297X-RAY DIFFRACTION100
1.5422-1.56340.20491860.14223288X-RAY DIFFRACTION100
1.5634-1.58570.19781620.14153344X-RAY DIFFRACTION100
1.5857-1.60940.21571770.14373317X-RAY DIFFRACTION100
1.6094-1.63450.2061840.13933291X-RAY DIFFRACTION100
1.6345-1.66130.19631690.13993321X-RAY DIFFRACTION100
1.6613-1.690.19851680.13673291X-RAY DIFFRACTION100
1.69-1.72070.20691600.13353339X-RAY DIFFRACTION100
1.7207-1.75380.19911750.12983316X-RAY DIFFRACTION100
1.7538-1.78960.17571990.12913266X-RAY DIFFRACTION100
1.7896-1.82850.17891660.13453307X-RAY DIFFRACTION100
1.8285-1.8710.19511580.13693334X-RAY DIFFRACTION100
1.871-1.91780.2091600.14053350X-RAY DIFFRACTION100
1.9178-1.96970.18151640.14333312X-RAY DIFFRACTION100
1.9697-2.02760.20671880.14563292X-RAY DIFFRACTION100
2.0276-2.09310.19161720.15153306X-RAY DIFFRACTION100
2.0931-2.16790.18491760.15413310X-RAY DIFFRACTION100
2.1679-2.25470.17881670.14983332X-RAY DIFFRACTION100
2.2547-2.35730.1881940.15243292X-RAY DIFFRACTION100
2.3573-2.48150.18551770.15233324X-RAY DIFFRACTION100
2.4815-2.63690.1821850.15873310X-RAY DIFFRACTION100
2.6369-2.84050.19991640.16553327X-RAY DIFFRACTION100
2.8405-3.12620.19341630.16573361X-RAY DIFFRACTION100
3.1262-3.57820.20581950.16513311X-RAY DIFFRACTION100
3.5782-4.50670.17791900.14883337X-RAY DIFFRACTION100
4.5067-36.06140.16581720.16393290X-RAY DIFFRACTION97

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