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- PDB-4y7d: Alpha/beta hydrolase fold protein from Nakamurella multipartita -

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Basic information

Entry
Database: PDB / ID: 4y7d
TitleAlpha/beta hydrolase fold protein from Nakamurella multipartita
ComponentsAlpha/beta hydrolase fold proteinAlpha/beta hydrolase superfamily
KeywordsHYDROLASE / Alpha/beta hydrolase / structural genomics / APC103603 / Midwest Center for Structural Genomics / PSI-Biology / MCSG
Function / homologyalpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Alpha/beta hydrolase fold protein
Function and homology information
Biological speciesNakamurella multipartita (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å
AuthorsCuff, M.E. / OSIPIUK, J. / Holowicki, J. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: to be published
Title: Alpha/beta hydrolase fold protein from Nakamurella multipartita.
Authors: Cuff, M.E. / OSIPIUK, J. / Holowicki, J. / Endres, M. / Joachimiak, A.
History
DepositionFeb 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta hydrolase fold protein
B: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2316
Polymers64,1142
Non-polymers1174
Water13,043724
1
A: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1153
Polymers32,0571
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1153
Polymers32,0571
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Alpha/beta hydrolase fold protein
hetero molecules

B: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2316
Polymers64,1142
Non-polymers1174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+3/2,-y+1,z+1/21
Buried area1400 Å2
ΔGint-54 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.404, 75.394, 126.536
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha/beta hydrolase fold protein / Alpha/beta hydrolase superfamily


Mass: 32056.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nakamurella multipartita (strain ATCC 700099 / DSM 44233 / JCM 9543 / Y-104) (bacteria)
Strain: ATCC 700099 / DSM 44233 / JCM 9543 / Y-104 / Gene: Namu_0557 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C8X7A4
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 724 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris Porpane -NaOH buffer, 1.2 M DL-malic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.68→36.1 Å / Num. all: 73782 / Num. obs: 73782 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.037 / Rrim(I) all: 0.091 / Χ2: 2.283 / Net I/av σ(I): 29.442 / Net I/σ(I): 14.3 / Num. measured all: 417774
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.68-1.713.40.6361.934580.7860.3860.7481.14595.4
1.71-1.7440.56636160.8620.3160.651.17398.5
1.74-1.774.30.5236340.8880.2780.5921.22599
1.77-1.814.60.42136280.9280.2170.4751.33299.7
1.81-1.854.90.38336350.9380.1910.4291.3899.6
1.85-1.895.30.3336680.9590.1580.3671.45999.5
1.89-1.945.80.26836670.9780.1220.2951.63599.9
1.94-1.9960.22436660.9810.10.2451.72999.9
1.99-2.0560.18736760.9830.0830.2051.87399.9
2.05-2.126.10.16236760.9860.0720.1781.94399.9
2.12-2.196.20.14336900.990.0630.1562.102100
2.19-2.286.20.13336690.9910.0580.1452.139100
2.28-2.386.30.1237010.9910.0520.1322.269100
2.38-2.516.30.10837000.9920.0470.1182.372100
2.51-2.676.40.09837290.9940.0420.1072.485100
2.67-2.876.40.08737120.9940.0380.0952.556100
2.87-3.166.40.07637570.9950.0330.0832.646100
3.16-3.626.40.06337570.9970.0270.0682.84199.9
3.62-4.566.30.05537910.9970.0240.063.37499.8
4.56-505.90.05939520.9960.0260.0655.53198.8

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.68→36.1 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.154 / SU ML: 0.068 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.187 3581 4.9 %RANDOM
Rwork0.1533 69609 --
obs0.1549 69609 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.38 Å2 / Biso mean: 26.598 Å2 / Biso min: 11.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å2-0 Å20 Å2
2--2.99 Å20 Å2
3----1.3 Å2
Refinement stepCycle: final / Resolution: 1.68→36.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4267 0 4 724 4995
Biso mean--27.57 37.94 -
Num. residues----577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194643
X-RAY DIFFRACTIONr_bond_other_d0.0070.024442
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9676358
X-RAY DIFFRACTIONr_angle_other_deg0.844310227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5745644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26722.407216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97815694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1051551
X-RAY DIFFRACTIONr_chiral_restr0.0960.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021102
X-RAY DIFFRACTIONr_mcbond_it1.0631.4212382
X-RAY DIFFRACTIONr_mcbond_other1.0551.422381
X-RAY DIFFRACTIONr_mcangle_it1.6532.1272993
LS refinement shellResolution: 1.679→1.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 249 -
Rwork0.259 4787 -
all-5036 -
obs--93.26 %
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)
11.2377-0.0897-0.29290.5916-0.19021.28840.0644-0.11710.02380.0042-0.0489-0.1202-0.08320.0657-0.01550.0956-0.01350.0130.042-0.01990.059425.890531.811269.2672
20.9646-0.06330.37991.3393-0.8441.4337-0.00110.11850.0131-0.0546-0.0003-0.04220.0410.05550.00140.09130.00520.00090.0165-0.00590.037734.13821.285927.2678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 502
2X-RAY DIFFRACTION2B11 - 502

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