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- PDB-3tp9: Crystal structure of Alicyclobacillus acidocaldarius protein with... -

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Basic information

Entry
Database: PDB / ID: 3tp9
TitleCrystal structure of Alicyclobacillus acidocaldarius protein with beta-lactamase and rhodanese domains
ComponentsBETA-LACTAMASE and RHODANESE DOMAIN PROTEIN
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / beta-lactamase domain / rhodanese domain
Function / homology
Function and homology information


Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A ...Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase domain protein
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsMichalska, K. / Chhor, G. / Mandel, M.E. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Alicyclobacillus acidocaldarius protein with beta-lactamase and rhodanese domains
Authors: Michalska, K. / Chhor, G. / Mandel, M.E. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE and RHODANESE DOMAIN PROTEIN
B: BETA-LACTAMASE and RHODANESE DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7904
Polymers103,6592
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-11 kcal/mol
Surface area36080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.335, 169.335, 77.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 470
2114B1 - 470

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Components

#1: Protein BETA-LACTAMASE and RHODANESE DOMAIN PROTEIN


Mass: 51829.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
Strain: DSM 446 / Gene: Aaci_0383 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: C8WS08
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris/HCl, 0.7 M sodium citrate tribasic, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2011 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 31713 / Num. obs: 30955 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 60.7 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 17.1
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1507 / % possible all: 96.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→37.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 29.871 / SU ML: 0.272 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25403 1238 4 %RANDOM
Rwork0.20272 ---
all0.20475 30812 --
obs0.20475 30812 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.982 Å2
Baniso -1Baniso -2Baniso -3
1--3.7 Å20 Å20 Å2
2---3.7 Å20 Å2
3---7.41 Å2
Refinement stepCycle: LAST / Resolution: 2.7→37.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7244 0 2 0 7246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217452
X-RAY DIFFRACTIONr_bond_other_d0.0010.025044
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.95310147
X-RAY DIFFRACTIONr_angle_other_deg0.842312194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7765945
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76222.714339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.071151123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4311568
X-RAY DIFFRACTIONr_chiral_restr0.0650.21096
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218485
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021571
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_it0.3581.54708
X-RAY DIFFRACTIONr_mcbond_other0.0621.51912
X-RAY DIFFRACTIONr_mcangle_it0.70627518
X-RAY DIFFRACTIONr_scbond_it1.49932744
X-RAY DIFFRACTIONr_scangle_it2.0454.52629
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 6103 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.220.5
medium thermal0.232
LS refinement shellResolution: 2.695→2.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 89 -
Rwork0.317 2005 -
obs-2005 91.04 %
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)
10.58880.32860.03899.1094-0.4463.20030.07490.13150.1552-0.27540.04460.0272-0.30160.0859-0.11950.0754-0.0360.04880.1242-0.0020.137344.84483.31246.7532
22.77570.74380.96322.33260.54422.34830.1189-0.1938-0.13780.1914-0.04450.24250.0188-0.1943-0.07440.0854-0.04110.07690.13250.0260.168631.2042-6.302250.6485
34.3308-3.5108-2.20144.8151.95213.05540.0252-0.4420.33680.32810.2989-0.64-0.17460.5887-0.32410.1014-0.0438-0.06930.2219-0.06310.173162.467-15.478950.3655
411.87674.07610.10354.39872.83736.3021-0.01140.2496-0.3640.4250.0779-0.28330.8525-0.1955-0.06650.2070.0132-0.01110.1040.04350.061658.1241-37.100839.824
54.8340.29482.61675.52423.83056.79870.0715-0.3311-0.29480.5144-0.1756-0.15350.6998-0.10760.10410.1523-0.04950.04360.14750.07820.124756.3831-36.057240.8202
61.4004-0.79510.12447.5138-0.0732.9960.0599-0.0842-0.25140.210.0441-0.05590.21290.028-0.10390.08820.0407-0.05280.1281-0.02920.120644.8533-3.424122.3732
73.3528-0.6215-1.29512.2120.71052.87950.08450.25750.2671-0.3853-0.00580.1812-0.1865-0.2591-0.07870.14890.0263-0.09270.15640.03750.200331.16886.143118.4002
84.66074.10961.95965.55531.84623.2231-0.08730.4997-0.3572-0.38850.3823-0.73480.26150.5592-0.2950.15670.05350.09890.2213-0.06640.212762.411215.428118.855
98.7138-2.99940.77934.28182.24195.7802-0.0036-0.10880.3506-0.36130.0716-0.2821-0.6576-0.1197-0.0680.142-0.04110.00920.09580.05270.084557.96237.073629.4606
104.9846-0.8933-3.54095.8114.09476.87050.08010.34310.15-0.3698-0.134-0.2288-0.3630.08280.05390.10740.0573-0.03990.14190.04710.134456.344935.930428.439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 66
2X-RAY DIFFRACTION2A67 - 242
3X-RAY DIFFRACTION3A243 - 358
4X-RAY DIFFRACTION4A359 - 412
5X-RAY DIFFRACTION5A413 - 471
6X-RAY DIFFRACTION6B-1 - 66
7X-RAY DIFFRACTION7B67 - 242
8X-RAY DIFFRACTION8B243 - 358
9X-RAY DIFFRACTION9B359 - 412
10X-RAY DIFFRACTION10B413 - 470

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