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- PDB-2f46: Crystal structure of a putative phosphatase (nma1982) from neisse... -

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Basic information

Entry
Database: PDB / ID: 2f46
TitleCrystal structure of a putative phosphatase (nma1982) from neisseria meningitidis z2491 at 1.41 A resolution
Componentshypothetical protein
KeywordsHYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Beta-lactamase hydrolase-like protein, phosphatase-like domain / Beta-lactamase hydrolase-like protein, phosphatase-like domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / : / DUF442 domain-containing protein
Similarity search - Component
Biological speciesNeisseria meningitidis Z2491 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.41 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 A resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases.
Authors: Krishna, S.S. / Tautz, L. / Xu, Q. / McMullan, D. / Miller, M.D. / Abdubek, P. / Ambing, E. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Chiu, H.J. / Clayton, T. / DiDonato, M. / Duan, L. ...Authors: Krishna, S.S. / Tautz, L. / Xu, Q. / McMullan, D. / Miller, M.D. / Abdubek, P. / Ambing, E. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Chiu, H.J. / Clayton, T. / DiDonato, M. / Duan, L. / Elsliger, M.A. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Han, G.W. / Haugen, J. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Koesema, E. / Morse, A.T. / Mustelin, T. / Nigoghossian, E. / Oommachen, S. / Reyes, R. / Rife, C.L. / van den Bedem, H. / Weekes, D. / White, A. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionNov 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE STRAIN CLONED DIFFERS FROM THE SEQUENCED STRAIN IN THE DATABASE. THE ELECTRON DENSITY CLEARLY INDICATED THAT VALINE AT 45 SHOULD BE ISOLEUCINE AND SERINE AT 102 SHOULD BE TYROSINE, I.E., V45I AND S102Y. THE DNA SEQUENCE OF THE CLONED CONSTRUCT CONFIRMS THIS OBSERVATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8835
Polymers35,8122
Non-polymers713
Water7,368409
1
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9412
Polymers17,9061
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9413
Polymers17,9061
Non-polymers352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.278, 33.466, 59.899
Angle α, β, γ (deg.)90.000, 96.180, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 15 - 153 / Label seq-ID: 16 - 154

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein hypothetical protein /


Mass: 17905.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis Z2491 (bacteria)
Species: Neisseria meningitidis / Strain: FAM18 / Gene: 7380613 / Plasmid: HK100:SpeedET / Production host: Escherichia coli (E. coli) / References: GenBank: 7380613, UniProt: A1KVD0*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.006356 Å3/Da / Density % sol: 38.694843 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.5
Details: 0.2M MgCl2, 30.0% PEG-4000, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.019951, 0.979741
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 11, 2005 / Details: COLLIMATING MIRROR, DCM, TOROIDAL FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0199511
20.9797411
ReflectionResolution: 1.41→18.62 Å / Num. obs: 46247 / % possible obs: 83.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 9
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value% possible all
1.41-1.4532.31.60.2762.513120.27632.3
1.45-1.4941.61.80.2213.316350.221
1.49-1.5354.420.1764.121060.176
1.53-1.5866.12.20.1395.224760.139
1.58-1.6379.22.40.1215.928390.121
1.63-1.6994.52.80.1066.533250.106
1.69-1.7599.73.10.0877.733990.087
1.75-1.8299.93.60.0777.832420.077
1.82-1.999.83.60.0688.531510.068
1.9-1.991003.60.065930120.065
1.99-2.199.93.60.0589.328440.058
2.1-2.231003.70.04810.727210.048
2.23-2.381003.60.0510.125600.05
2.38-2.571003.60.0412.223880.04
2.57-2.821003.60.03912.521850.039
2.82-3.151003.60.03513.519760.035
3.15-3.6499.93.50.03315.217730.033
3.64-4.4699.43.40.03116.314960.031
4.46-6.3199.83.30.02816.411770.028
6.31-18.6292.430.0315.46300.03

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.41→18.62 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.719 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.089
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THERE EXISTS A PSEUDO-TRANSLATION BETWEEN THE TWO MONOMERS IN THE ASU. AS A RESULT, THE L=2N+1 REFLECTIONS ARE SYSTEMATICALLY WEAK. ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THERE EXISTS A PSEUDO-TRANSLATION BETWEEN THE TWO MONOMERS IN THE ASU. AS A RESULT, THE L=2N+1 REFLECTIONS ARE SYSTEMATICALLY WEAK. THIS RESULTS IN HIGH R-FACTOR FOR L=2N+1 REFLECTIONS. THE OVERALL R-FACTORS IS RELATIVELY HIGH DUE TO THIS REASON. THE MAPS LOOK VERY GOOD. 3. AN UNKNOWN DENSITY NEAR B88 WAS MODELED AS UNL, UNKNOWN LIGAND. 4. DATA AT HIGHEST RESOLUTION SHELLS ARE INCOMPLETE.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2352 5.1 %RANDOM
Rwork0.2 ---
all0.201 ---
obs0.20104 43885 83.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.814 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-0.39 Å2
2--0.32 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.41→18.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 7 409 2655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222515
X-RAY DIFFRACTIONr_bond_other_d0.0020.022293
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9433433
X-RAY DIFFRACTIONr_angle_other_deg0.83735311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1285330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03923.383133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05415440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2221529
X-RAY DIFFRACTIONr_chiral_restr0.0790.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022957
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02550
X-RAY DIFFRACTIONr_nbd_refined0.2620.2576
X-RAY DIFFRACTIONr_nbd_other0.1950.22541
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21301
X-RAY DIFFRACTIONr_nbtor_other0.0830.21476
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2302
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.234
X-RAY DIFFRACTIONr_mcbond_it1.95931584
X-RAY DIFFRACTIONr_mcbond_other0.5023618
X-RAY DIFFRACTIONr_mcangle_it2.90352512
X-RAY DIFFRACTIONr_scbond_it4.58781028
X-RAY DIFFRACTIONr_scangle_it6.44711915
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2124 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.275
LOOSE THERMAL1.2510
LS refinement shellResolution: 1.41→1.447 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 67 -
Rwork0.286 1247 -
obs--32.3 %

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