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- PDB-2wm3: Crystal structure of NmrA-like family domain containing protein 1... -

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Basic information

Entry
Database: PDB / ID: 2wm3
TitleCrystal structure of NmrA-like family domain containing protein 1 in complex with niflumic acid
ComponentsNMRA-LIKE FAMILY DOMAIN CONTAINING PROTEIN 1
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


Urea cycle / perinuclear region of cytoplasm / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-NFL / PHOSPHATE ION / NmrA-like family domain-containing protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBhatia, C. / Yue, W.W. / Niesen, F. / Pilka, E. / Ugochukwu, E. / Savitsky, P. / Hozjan, V. / Roos, A.K. / Filippakopoulos, P. / von Delft, F. ...Bhatia, C. / Yue, W.W. / Niesen, F. / Pilka, E. / Ugochukwu, E. / Savitsky, P. / Hozjan, V. / Roos, A.K. / Filippakopoulos, P. / von Delft, F. / Heightman, T. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid
Authors: Bhatia, C. / Yue, W.W. / Pilka, E. / Ugochukwu, E. / Savitsky, P. / Hozjan, V. / Roos, A.K. / Filippakopoulos, P. / von Delft, F. / Heightman, T. / Arrowsmith, C. / Weigelt, J. / Edwards, A. ...Authors: Bhatia, C. / Yue, W.W. / Pilka, E. / Ugochukwu, E. / Savitsky, P. / Hozjan, V. / Roos, A.K. / Filippakopoulos, P. / von Delft, F. / Heightman, T. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
History
DepositionJun 29, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 5, 2012Group: Database references / Non-polymer description ...Database references / Non-polymer description / Other / Source and taxonomy / Structure summary
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NMRA-LIKE FAMILY DOMAIN CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8947
Polymers33,3631
Non-polymers1,5306
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.712, 68.712, 183.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NMRA-LIKE FAMILY DOMAIN CONTAINING PROTEIN 1


Mass: 33363.293 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9HBL8

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Non-polymers , 6 types, 275 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-NFL / 2-{[3-(TRIFLUOROMETHYL)PHENYL]AMINO}NICOTINIC ACID / 2-[(3-TRIFLUOROMETHYL)PHENYL]AMINO-3-PYRIDINE-CARBOXYLIC ACID / Niflumic acid


Mass: 282.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9F3N2O2 / Comment: inhibitor*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 3.26 Å3/Da / Density % sol: 62.24 % / Description: NONE
Crystal growDetails: 2.1M SODIUM MALATE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9764
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 2008
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.85→55.05 Å / Num. obs: 38676 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.6
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.651 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19709 1934 5 %RANDOM
Rwork0.16579 ---
obs0.16734 36707 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.514 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 100 269 2659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222496
X-RAY DIFFRACTIONr_bond_other_d0.0010.021663
X-RAY DIFFRACTIONr_angle_refined_deg2.1162.033397
X-RAY DIFFRACTIONr_angle_other_deg0.9393.0024017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1255300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.09423.704108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8515404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4151518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212764
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02498
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_it0.8621.51483
X-RAY DIFFRACTIONr_mcbond_other0.2681.5608
X-RAY DIFFRACTIONr_mcangle_it1.55222379
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.61231013
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1524.51017
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 145 -
Rwork0.301 2627 -
obs--99.04 %
Refinement TLS params.Method: refined / Origin x: 64.601 Å / Origin y: 20.3618 Å / Origin z: 81.9178 Å
111213212223313233
T0.0453 Å20.0519 Å2-0.0089 Å2-0.1161 Å2-0.0231 Å2--0.0458 Å2
L1.4425 °20.2341 °20.2736 °2-0.756 °20.2645 °2--1.3004 °2
S-0.1084 Å °-0.1286 Å °-0.0019 Å °0.1291 Å °0.059 Å °-0.0215 Å °0.0061 Å °-0.0104 Å °0.0494 Å °

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