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- PDB-4dun: 1.76A X-ray Crystal Structure of a Putative Phenazine Biosynthesi... -

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Basic information

Entry
Database: PDB / ID: 4dun
Title1.76A X-ray Crystal Structure of a Putative Phenazine Biosynthesis PhzC/PhzF Protein from Clostridium difficile (strain 630)
ComponentsPutative phenazine biosynthesis PhzC/PhzF protein
KeywordsBIOSYNTHETIC PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


biosynthetic process / catalytic activity
Similarity search - Function
Phenazine biosynthesis PhzF protein / Phenazine biosynthesis-like protein / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Putative phenazine biosynthesis PhzC/PhzF protein
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsBrunzelle, J.S. / Wawrzak, W. / Kudritska, M. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.76A X-ray Crystal Structure of a Putative Phenazine Biosynthesis PhzC/PhzF Protein from Clostridium difficile (strain 630)
Authors: Brunzelle, J.S. / Wawrzak, W. / Kudritska, M. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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: Putative phenazine biosynthesis PhzC/PhzF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0835
Polymers29,5101
Non-polymers5734
Water6,666370
1
A: Putative phenazine biosynthesis PhzC/PhzF protein
hetero molecules

A: Putative phenazine biosynthesis PhzC/PhzF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,16610
Polymers59,0202
Non-polymers1,1468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4240 Å2
ΔGint-57 kcal/mol
Surface area23050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.650, 63.650, 135.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-540-

HOH

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Components

#1: Protein Putative phenazine biosynthesis PhzC/PhzF protein


Mass: 29509.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD1761, CD630_17610 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q186X0
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 3350 20% w/v, Na Sulfate 0.2M, Bis-Tris 0.1M pH5.5, 2% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2012 / Details: Be Lens
RadiationMonochromator: Single Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.76→51.04 Å / Num. all: 32236 / Num. obs: 32236 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 25.68 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.9
Reflection shellResolution: 1.76→1.81 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2336 / % possible all: 100

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
PHASERphasing
PHENIXmodel building
BUSTER2.8.0refinement
XDSdata reduction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1S7J

1s7j


Resolution: 1.76→23.12 Å / Cor.coef. Fo:Fc: 0.9662 / Cor.coef. Fo:Fc free: 0.9498 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1630 5.07 %RANDOM
Rwork0.158 ---
all0.1597 33802 --
obs0.158 32172 --
Displacement parametersBiso mean: 30.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.2868 Å20 Å20 Å2
2--0.2868 Å20 Å2
3----0.5737 Å2
Refine analyzeLuzzati coordinate error obs: 0.183 Å
Refinement stepCycle: LAST / Resolution: 1.76→23.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 34 370 2445
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012230HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.093040HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1039SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes62HARMONIC2
X-RAY DIFFRACTIONt_gen_planes322HARMONIC5
X-RAY DIFFRACTIONt_it2204HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.11
X-RAY DIFFRACTIONt_other_torsion2.55
X-RAY DIFFRACTIONt_chiral_improper_torsion294SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2862SEMIHARMONIC4
LS refinement shellResolution: 1.76→1.82 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2491 145 4.95 %
Rwork0.2031 2782 -
all0.2054 2927 -
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)
11.80980.12340.75760.68920.46930.3966-0.0785-0.07310.1441-0.04340.0046-0.1258-0.1053-0.0540.0739-0.06290.02560.0094-0.0572-0.0018-0.063710.94936.760463.8394
23.4739-0.3781-2.45770.77141.23022.8182-0.0380.26490.0829-0.1191-0.0109-0.031-0.11840.17290.04890.03530.00680.01590.08480.0103-0.005223.766929.192551.1958
33.32960.744-0.72832.0293-1.08352.56920.00780.34040.2459-0.21060.0294-0.12990.05570.0183-0.03710.0210.01080.04120.03850.01550.027317.261231.95156.0585
41.3006-0.99930.0672.62840.18161.3433-0.04830.04730.12110.0288-0.0264-0.164-0.05860.0240.0747-0.05140.00940.0233-0.0418-0.011-0.063511.354336.711254.4799
52.5436-1.2907-0.20320.6823-0.65380.82250.10950.18640.0916-0.1004-0.1482-0.0012-0.1443-0.12640.0387-0.00480.01810.0055-0.03-0.02480.00683.40441.438450.3394
61.5575-0.10610.70570.91481.1131.150.07630.1623-0.3166-0.0701-0.0687-0.01850.3029-0.3251-0.00760.0223-0.08820.0022-0.0098-0.0265-0.0135-16.662219.204552.1205
73.6960.32070.61520.15460.3662.2669-0.0446-0.0529-0.4026-0.00630.10650.02970.3916-0.1265-0.0619-0.0357-0.0390.0064-0.05080.0118-0.0103-14.530918.609758.6285
82.694-0.2181-1.06883.2198-0.15993.8741-0.0374-0.1247-0.4404-0.0471-0.0623-0.07230.42160.03360.0997-0.032-0.02840.0239-0.01410.0156-0.0037-9.595920.070964.3574
93.23480.22120.28171.5909-1.19521.9257-0.0385-0.007-0.1547-0.05650.0122-0.05650.10770.01910.0264-0.0381-0.01110.0191-0.0326-0.0132-0.0768-7.051527.614660.1746
102.17230.7128-0.51870.7309-0.2781.87890.0193-0.0650.11480.03360.08610.2421-0.1245-0.2693-0.1054-0.04350.00460.0218-0.0098-0.0158-0.0409-11.049537.123860.3797
116.59530.01523.06380.8417-0.29032.4932-0.1130.04530.1201-0.10110.0513-0.0792-0.01390.00510.06160.0317-0.01770.0146-0.0408-0.01750.01587.923638.952158.9779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 24}A1 - 24
2X-RAY DIFFRACTION2{A|25 - 35}A25 - 35
3X-RAY DIFFRACTION3{A|36 - 54}A36 - 54
4X-RAY DIFFRACTION4{A|55 - 88}A55 - 88
5X-RAY DIFFRACTION5{A|89 - 114}A89 - 114
6X-RAY DIFFRACTION6{A|115 - 126}A115 - 126
7X-RAY DIFFRACTION7{A|127 - 148}A127 - 148
8X-RAY DIFFRACTION8{A|149 - 181}A149 - 181
9X-RAY DIFFRACTION9{A|182 - 212}A182 - 212
10X-RAY DIFFRACTION10{A|213 - 237}A213 - 237
11X-RAY DIFFRACTION11{A|238 - 258}A238 - 258

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