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- PDB-2p97: CRYSTAL STRUCTURE OF A PUTATIVE METAL-DEPENDENT HYDROLASE (AVA_30... -

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Entry
Database: PDB / ID: 2p97
TitleCRYSTAL STRUCTURE OF A PUTATIVE METAL-DEPENDENT HYDROLASE (AVA_3068) FROM ANABAENA VARIABILIS ATCC 29413 AT 1.65 A RESOLUTION
ComponentsHypothetical protein
KeywordsMETAL BINDING PROTEIN / PUTATIVE METAL-DEPENDENT HYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyMetallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / metal ion binding / Alpha Beta / Metallo-beta-lactamase domain-containing protein
Function and homology information
Biological speciesAnabaena variabilis ATCC 29413 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (YP_323572.1) from Anabaena variabilis ATCC 29413 at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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
Revision 1.5Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999 SEQUENCE 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.

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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)45,1775
Polymers45,0932
Non-polymers843
Water9,314517
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-30 kcal/mol
Surface area16510 Å2
MethodPISA
2
A: Hypothetical protein
B: Hypothetical protein
hetero molecules

A: Hypothetical protein
B: Hypothetical protein
hetero molecules

A: Hypothetical protein
B: Hypothetical protein
hetero molecules

A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,70720
Polymers180,3708
Non-polymers33612
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area15860 Å2
ΔGint-152 kcal/mol
Surface area59780 Å2
MethodPISA
3
A: Hypothetical protein
B: Hypothetical protein
hetero molecules

A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,35310
Polymers90,1854
Non-polymers1686
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5960 Å2
ΔGint-71 kcal/mol
Surface area31860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.320, 103.320, 96.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

21A-209-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYTHRTHR5AA0 - 141 - 15
21GLYGLYTHRTHR5BB0 - 141 - 15
32GLYGLYGLUGLU5AA25 - 8726 - 88
42GLYGLYGLUGLU5BB25 - 8726 - 88
53LYSLYSTYRTYR1AA88 - 9489 - 95
63LYSLYSTYRTYR1BB88 - 9489 - 95
74CYSCYSALAALA5AA95 - 20096 - 201
84CYSCYSALAALA5BB95 - 20096 - 201

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Components

#1: Protein Hypothetical protein


Mass: 22546.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria)
Species: Anabaena variabilis / Strain: PCC 7937 / Gene: YP_323572.1, Ava_3068 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3M8K9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.8656.99THE STRUCTURE WAS SOLVED BY MAD METHOD USING A DIFFERENT CRYSTAL. THE PHASE RESTRAINTS FROM THAT CRYSTAL WERE USED IN THE CURRENT REFINEMENT
2THE STRUCTURE WAS SOLVED BY MAD METHOD USING A DIFFERENT CRYSTAL. THE PHASE RESTRAINTS FROM THAT CRYSTAL WERE USED IN THE CURRENT REFINEMENT
Crystal grow
Temperature (K)Crystal-IDMethodDetailspH
2771vapor diffusion, sitting dropNANODROP, 15.8% PEG 3350, 0.186M Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2932vapor diffusion, sitting dropNANODROP, 20.0% PEG 3350, 0.2M Magnesium nitrate, 0.1M MES pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.97927
SYNCHROTRONSSRL BL11-120.97920, 0.91162, 0.97898
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDFeb 15, 2007Flat collimating mirror, toroid focusing mirror
MARMOSAIC 325 mm CCD2CCDFeb 11, 2007Flat mirror (vertical focusing)
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2Single crystal Si(111) bent (horizontal focusing)
Radiation wavelength
IDWavelength (Å)Relative weight
10.979271
20.97921
30.911621
40.978981
ReflectionResolution: 1.65→29.488 Å / Num. obs: 63319 / % possible obs: 96.4 % / Biso Wilson estimate: 29.985 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.57
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.65-1.710.6262.3408471083888.7
1.71-1.780.5012.9431341135692.5
1.78-1.860.3594425361116194.3
1.86-1.960.2515.6448741177496.3
1.96-2.080.1688.2437941141397.3
2.08-2.240.11411.6454131180698.5
2.24-2.460.08315.2448851164299
2.46-2.820.05920.1467801214499.3
2.820.03430.9462231196499.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→29.488 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.225 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.081
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TWO MAGNESIUM IONS FROM CRYSTALLIZATION ARE MODELED IN SUBUNIT. 5. ONE CHLORIDE ION FROM CRYSTALLIZATION WAS MODELED. 6. THERE IS A DUAL CONFORMATION IN SUBUNIT A FROM RESIDUE 16 TO 23.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 3211 5.1 %RANDOM
Rwork0.16 ---
all0.162 ---
obs0.162 63263 99.83 %-
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: 28.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---0.59 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 3 517 3647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223513
X-RAY DIFFRACTIONr_bond_other_d0.0020.023276
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9644813
X-RAY DIFFRACTIONr_angle_other_deg0.94737598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5925461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70323.701154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.77115607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2921528
X-RAY DIFFRACTIONr_chiral_restr0.0990.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024027
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02725
X-RAY DIFFRACTIONr_nbd_refined0.2110.3629
X-RAY DIFFRACTIONr_nbd_other0.1780.33332
X-RAY DIFFRACTIONr_nbtor_refined0.1730.51660
X-RAY DIFFRACTIONr_nbtor_other0.0830.52133
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.5628
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0660.52
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.36
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.327
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.551
X-RAY DIFFRACTIONr_mcbond_it1.89532356
X-RAY DIFFRACTIONr_mcbond_other0.5563886
X-RAY DIFFRACTIONr_mcangle_it2.33153553
X-RAY DIFFRACTIONr_scbond_it4.65481479
X-RAY DIFFRACTIONr_scangle_it5.862111255
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
112TIGHT POSITIONAL0.050.05
1016MEDIUM POSITIONAL0.170.5
1637LOOSE POSITIONAL0.55
112TIGHT THERMAL0.370.5
1016MEDIUM THERMAL0.822
1637LOOSE THERMAL210
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 217 -
Rwork0.239 4369 -
obs-4586 99.01 %
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)
10.76920.1415-0.07550.9637-0.24851.03980.01440.0990.1267-0.1424-0.00550.0486-0.0619-0.0941-0.0089-0.12530.0169-0.0046-0.17150.0195-0.17633.819.5328.798
21.0788-0.17050.10821.37530.31561.73540.00390.0341-0.0172-0.12680.0892-0.2307-0.10250.1827-0.0931-0.159-0.01940.0646-0.1477-0.0014-0.115131.7026.00933.07
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 0 - 200 / Label seq-ID: 1 - 201

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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