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- PDB-7sua: Crystal Structure of the Hypothetical Protein (ACX60_00475) from ... -

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Basic information

Entry
Database: PDB / ID: 7sua
TitleCrystal Structure of the Hypothetical Protein (ACX60_00475) from Acinetobacter baumannii
ComponentsDUF4175 domain-containing protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Center for Structural Biology of Infectious Diseases / CSBID
Function / homologymembrane / DI(HYDROXYETHYL)ETHER / DUF4175 domain-containing protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To be Published
Title: Crystal Structure of the Hypothetical Protein (ACX60_00475) from Acinetobacter baumannii
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Other / Structure summary / Category: audit_author / pdbx_SG_project / struct_keywords
Item: _audit_author.name / _pdbx_SG_project.full_name_of_center ..._audit_author.name / _pdbx_SG_project.full_name_of_center / _pdbx_SG_project.initial_of_center / _struct_keywords.text
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF4175 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0133
Polymers31,8451
Non-polymers1682
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.755, 59.784, 75.625
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 DUF4175 domain-containing protein


Mass: 31845.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: C2U32_13765, C5H40_02315, CPI82_04650, CTZ19_00475, D8O08_001740, DLI71_12185, DLI72_04775, E1A87_06460, E2535_11650, E2539_19140, EA706_08735, EA720_011135, EA722_13985, EKS29_19110, EP550_ ...Gene: C2U32_13765, C5H40_02315, CPI82_04650, CTZ19_00475, D8O08_001740, DLI71_12185, DLI72_04775, E1A87_06460, E2535_11650, E2539_19140, EA706_08735, EA720_011135, EA722_13985, EKS29_19110, EP550_00510, EP560_17500, F2P40_11735, F4T85_08810, F4T91_09080, FE003_00465, FJU36_16290, FJU42_18320, FR761_00435, GSE42_19580, H0529_16845, HBK86_17525, IMO23_17555
Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: A0A237U7Y1
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.8 Å3/Da / Density % sol: 31.72 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 8.8 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: Classics II (D10), 0.1M Bis-Tris (pH 6.5), 20% (w/v) PEG5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 22, 2019 / Details: Be
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 27958 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.037 / Rrim(I) all: 0.079 / Rsym value: 0.069 / Χ2: 1.572 / Net I/σ(I): 24.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1354 / CC1/2: 0.71 / CC star: 0.911 / Rpim(I) all: 0.379 / Rrim(I) all: 0.787 / Rsym value: 0.687 / Χ2: 1 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→27.06 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.616 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 1376 4.9 %RANDOM
Rwork0.1759 ---
obs0.1775 26532 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.08 Å2 / Biso mean: 25.796 Å2 / Biso min: 13.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0 Å2
2---0.39 Å20 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 1.65→27.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1539 0 11 251 1801
Biso mean--48.97 36.06 -
Num. residues----195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131717
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171654
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.6432341
X-RAY DIFFRACTIONr_angle_other_deg0.3421.5773824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0655229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.81423.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.96515295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.337158
X-RAY DIFFRACTIONr_chiral_restr0.0630.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.022013
X-RAY DIFFRACTIONr_gen_planes_other0.0490.02395
LS refinement shellResolution: 1.655→1.697 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 87 -
Rwork0.265 1833 -
all-1920 -
obs--94.81 %
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)
11.5484-0.3067-0.4971.84281.11711.8682-0.078-0.0774-0.01980.03110.02060.0235-0.02930.08940.05740.01880.00740.01260.01860.01540.02057.315711.42259.4423
21.5496-0.3554-0.13181.9626-0.61822.3215-0.0390.0275-0.1650.00940.00760.03860.05550.10140.03140.00380.0060.00850.02570.00750.02866.52126.6076.8156
31.0074-0.47981.37081.0291-0.64674.1458-0.0566-0.0432-0.03240.07110.02420.11260.008-0.16930.03240.01090.00360.0160.01940.01240.0321-2.053110.71147.9612
41.87710.1638-0.40892.6407-0.12978.49110.00260.1197-0.0984-0.18440.10380.27840.6728-0.0013-0.10640.0664-0.0067-0.02920.02570.00450.0472-4.62892.08871.0287
54.9347-3.61972.44094.5413-2.51132.70970.1010.1353-0.5211-0.20070.09280.2910.2962-0.1105-0.19380.0607-0.0419-0.03580.04440.00350.1308-6.7586-2.27562.5528
67.93922.87782.50848.12293.46112.88570.066-0.2702-0.4140.36220.0017-0.51610.24470.1133-0.06760.02630.02230.00130.07440.07490.109713.4083-3.381513.1137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A220 - 274
2X-RAY DIFFRACTION2A275 - 316
3X-RAY DIFFRACTION3A317 - 348
4X-RAY DIFFRACTION4A349 - 369
5X-RAY DIFFRACTION5A370 - 400
6X-RAY DIFFRACTION6A401 - 414

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