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- PDB-4iag: Crystal structure of ZbmA, the zorbamycin binding protein from St... -

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Basic information

Entry
Database: PDB / ID: 4iag
TitleCrystal structure of ZbmA, the zorbamycin binding protein from Streptomyces flavoviridis
ComponentsZbm binding protein
KeywordsZorbamycin Binding Protein / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro / BLMA_like / zorbamycin / reductive isopropylation
Function / homologyBleomycin resistance protein / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / response to antibiotic / Roll / Alpha Beta / Zbm binding protein
Function and homology information
Biological speciesStreptomyces flavoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsCuff, M.E. / Bigelow, L. / Bruno, C.J.P. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. ...Cuff, M.E. / Bigelow, L. / Bruno, C.J.P. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Biochemistry / Year: 2015
Title: Crystal Structure of the Zorbamycin-Binding Protein ZbmA, the Primary Self-Resistance Element in Streptomyces flavoviridis ATCC21892.
Authors: Rudolf, J.D. / Bigelow, L. / Chang, C. / Cuff, M.E. / Lohman, J.R. / Chang, C.Y. / Ma, M. / Yang, D. / Clancy, S. / Babnigg, G. / Joachimiak, A. / Phillips, G.N. / Shen, B.
History
DepositionDec 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Structure summary
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Dec 2, 2015Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Revision 1.5Mar 26, 2025Group: 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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: Zbm binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,60410
Polymers15,0151
Non-polymers5899
Water99155
1
A: Zbm binding protein
hetero molecules

A: Zbm binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,20820
Polymers30,0312
Non-polymers1,17718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area5910 Å2
ΔGint9 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.787, 38.787, 268.524
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
DetailsLikely forms a dimer with the crystallographic symmetry mate: x,y,z and 1-y, 1-x, 1/6-z.

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Components

#1: Protein Zbm binding protein


Mass: 15015.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces flavoviridis (bacteria) / Strain: ATCC 21892 / Gene: zbmA / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: B9UIZ4
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LYSINE RESIDUES IN THIS PROTEIN WERE SUBJECT TO REDUCTIVE ISOPROPYLATION
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: 1.97 Å3/Da / Density % sol: 37.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: protein subject to reductive isopropylation, 0.8M Ammonium Sulfate, 0.1M Sodium Sitrate: HCl pH 4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 3, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionRedundancy: 9.7 % / Av σ(I) over netI: 33.01 / Number: 101644 / Rmerge(I) obs: 0.068 / Χ2: 1.23 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 10484 / % possible obs: 98.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.165097.110.0572.1848.9
4.095.1699.710.0471.61510.6
3.584.0910010.051.52411.1
3.253.5810010.0551.5412
3.023.2510010.0671.4211.8
2.843.0210010.0741.14712.4
2.72.8410010.091.20212.2
2.582.710010.1051.10112.4
2.482.5810010.1181.15312.4
2.392.4810010.1171.02712.4
2.322.3910010.1290.98811.7
2.252.3210010.1781.20410.6
2.192.2510010.1860.989.8
2.142.1910010.2230.8989.4
2.092.1410010.2770.8478.2
2.052.0999.810.3150.9316.6
2.012.0597.910.3480.776
1.972.0195.410.3720.8675
1.931.9793.210.3970.8464.3
1.91.9387.510.4340.914
ReflectionResolution: 1.9→50 Å / Num. all: 10484 / Num. obs: 10484 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.068 / Χ2: 1.225 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.9340.4344600.91187.5
1.93-1.974.30.3974630.846193.2
1.97-2.0150.3724720.867195.4
2.01-2.0560.3485180.77197.9
2.05-2.096.60.3154960.931199.8
2.09-2.148.20.2775030.8471100
2.14-2.199.40.2235120.8981100
2.19-2.259.80.1865200.981100
2.25-2.3210.60.1785091.2041100
2.32-2.3911.70.1295150.9881100
2.39-2.4812.40.1175121.0271100
2.48-2.5812.40.1185351.1531100
2.58-2.712.40.1055211.1011100
2.7-2.8412.20.095241.2021100
2.84-3.0212.40.0745361.1471100
3.02-3.2511.80.0675451.421100
3.25-3.58120.0555391.541100
3.58-4.0911.10.055531.5241100
4.09-5.1610.60.0475871.615199.7
5.16-508.90.0576642.184197.1

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2 Å / D res low: 44.75 Å / FOM : 0.172 / FOM acentric: 0.248 / FOM centric: 0 / Reflection: 9000 / Reflection acentric: 6258 / Reflection centric: 2742
Phasing MAD setR cullis acentric: 2.07 / R cullis centric: 1 / Highest resolution: 2 Å / Lowest resolution: 44.75 Å / Loc acentric: 0 / Loc centric: 0 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 6258 / Reflection centric: 2742
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.19-44.753.950.30.1653
7.05-12.192.230.10.174134
4.96-7.052.460.10213217
3.83-4.961.30.10.1432308
3.12-3.831.490.10746391
2.63-3.122.680.101113470
2.27-2.632.78001558548
2-2.272.38002116621
Phasing MAD set siteAtom type symbol: Se / B iso: 53.9197 / Fract x: 0.914 / Fract y: 0.714 / Fract z: 0.017 / Occupancy: 4.23 / Occupancy iso: 0
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.19-44.750.0410.406059653
7.05-12.190.1650.463020874134
4.96-7.050.2610.5270430213217
3.83-4.960.250.4280740432308
3.12-3.830.2750.41801137746391
2.63-3.120.250.355015831113470
2.27-2.630.1560.211021061558548
2-2.270.0650.084027372116621
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 10313
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.58-10073.90.488506
4.35-5.5870.60.807506
3.76-4.3569.50.829506
3.39-3.7670.40.825503
3.14-3.39720.803502
2.94-3.1469.80.777507
2.78-2.9470.50.767505
2.65-2.7872.20.751509
2.54-2.6576.30.735501
2.45-2.5481.30.745506
2.37-2.4579.20.685511
2.3-2.3781.20.719502
2.23-2.384.90.747507
2.18-2.2380.80.754512
2.12-2.1891.60.777522
2.08-2.1282.50.698506
2.03-2.0885.20.71515
1.99-2.0387.20.684501
1.95-1.9991.50.633507
1.9-1.9588.70.565679

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→32.59 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2317 / WRfactor Rwork: 0.1832 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8678 / SU B: 7.7 / SU ML: 0.107 / SU R Cruickshank DPI: 0.1613 / SU Rfree: 0.1483 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.148
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 492 4.8 %RANDOM
Rwork0.1893 ---
all0.1913 10243 --
obs0.1913 10243 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.97 Å2 / Biso mean: 38.2635 Å2 / Biso min: 20.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20.57 Å20 Å2
2--0.57 Å20 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 38 55 1039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191021
X-RAY DIFFRACTIONr_bond_other_d0.0050.02968
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.9671379
X-RAY DIFFRACTIONr_angle_other_deg1.3983.0112219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0925126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80123.8347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40315140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.541157
X-RAY DIFFRACTIONr_chiral_restr0.1090.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211133
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02232
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 36 -
Rwork0.285 639 -
all-675 -
obs--90 %
Refinement TLS params.Method: refined / Origin x: 46.1737 Å / Origin y: -2.9324 Å / Origin z: 32.3225 Å
111213212223313233
T0.1502 Å2-0.1359 Å20.0278 Å2-0.1598 Å20.0037 Å2--0.062 Å2
L1.9312 °20.6523 °20.1694 °2-1.7258 °20.2261 °2--1.4975 °2
S0.2655 Å °-0.3032 Å °0.0669 Å °0.1092 Å °-0.2601 Å °0.0033 Å °0.056 Å °0.0276 Å °-0.0054 Å °

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