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- PDB-1mmo: CRYSTAL STRUCTURE OF A BACTERIAL NON-HAEM IRON HYDROXYLASE THAT C... -

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Basic information

Entry
Database: PDB / ID: 1mmo
TitleCRYSTAL STRUCTURE OF A BACTERIAL NON-HAEM IRON HYDROXYLASE THAT CATALYSES THE BIOLOGICAL OXIDATION OF METHANE
Components(METHANE MONOOXYGENASE HYDROLASE ...) x 3
KeywordsOXIDOREDUCTASE (MONOOXYGENASE)
Function / homology
Function and homology information


methane metabolic process / methane monooxygenase (soluble) / methane monooxygenase [NAD(P)H] activity / one-carbon metabolic process / metal ion binding
Similarity search - Function
Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / : / : / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / Methane monooxygenase, hydrolase gamma chain / Methane/phenol monooxygenase, hydroxylase component ...Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / : / : / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / Methane monooxygenase, hydrolase gamma chain / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Monooxygenase / Ribonucleotide reductase-like / Ferritin-like superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / : / Methane monooxygenase component A gamma chain / Methane monooxygenase component A beta chain / Methane monooxygenase component A alpha chain
Similarity search - Component
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsRosenzweig, A.C. / Frederick, C.A. / Lippard, S.J. / Nordlund, P.
CitationJournal: Nature / Year: 1993
Title: Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological oxidation of methane.
Authors: Rosenzweig, A.C. / Frederick, C.A. / Lippard, S.J. / Nordlund, P.
History
DepositionFeb 22, 1994Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_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_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.pdbx_dist_value / _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.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
Remark 650HELIX IN *HELIX* RECORDS BELOW, HELIX IDENTIFIERS WHICH BEGIN WITH THE LETTER "D" OR "E" DENOTE THE ...HELIX IN *HELIX* RECORDS BELOW, HELIX IDENTIFIERS WHICH BEGIN WITH THE LETTER "D" OR "E" DENOTE THE A SUBUNIT. HELIX IDENTIFIERS WHICH BEGIN WITH THE LETTER "B" OR "C" DENOTE THE B SUBUNIT. HELIX IDENTIFIERS WHICH BEGIN WITH THE LETTER "G" OR "H" DENOTE THE G SUBUNIT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: METHANE MONOOXYGENASE HYDROLASE (BETA CHAIN)
C: METHANE MONOOXYGENASE HYDROLASE (BETA CHAIN)
D: METHANE MONOOXYGENASE HYDROLASE (ALPHA CHAIN)
E: METHANE MONOOXYGENASE HYDROLASE (ALPHA CHAIN)
G: METHANE MONOOXYGENASE HYDROLASE (GAMMA CHAIN)
H: METHANE MONOOXYGENASE HYDROLASE (GAMMA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,69312
Polymers245,3506
Non-polymers3436
Water15,475859
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40230 Å2
ΔGint-205 kcal/mol
Surface area62900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.600, 110.100, 333.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: ALA D 19 - PRO D 20 OMEGA = 149.54 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ALA E 19 - PRO E 20 OMEGA = 146.10 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO G 121 / 4: CIS PROLINE - PRO H 121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9999, -0.00538, -0.00427), (-0.00198, -0.36884, 0.92949), (-0.0065, 0.92947, 0.36882)
Vector: 84.26408, 27.26639, -18.08793)
DetailsTHERE IS A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS RELATING THE ABG PAIRS IN THE DIMER. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS C, E, AND H WHEN APPLIED TO CHAINS B, D, AND G, RESPECTIVELY.

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Components

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METHANE MONOOXYGENASE HYDROLASE ... , 3 types, 6 molecules BCDEGH

#1: Protein METHANE MONOOXYGENASE HYDROLASE (BETA CHAIN)


Mass: 44452.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (bacteria)
References: UniProt: P18798, methane monooxygenase (soluble)
#2: Protein METHANE MONOOXYGENASE HYDROLASE (ALPHA CHAIN)


Mass: 59241.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (bacteria)
References: UniProt: P22869, methane monooxygenase (soluble)
#3: Protein METHANE MONOOXYGENASE HYDROLASE (GAMMA CHAIN)


Mass: 18980.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (bacteria)
References: UniProt: P11987, methane monooxygenase (soluble)

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Non-polymers , 3 types, 865 molecules

#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 859 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsIN *TURN* RECORDS BELOW, TURN IDENTIFIERS WHICH BEGIN WITH THE LETTER "D" OR "E" CORRESPOND TO THE ...IN *TURN* RECORDS BELOW, TURN IDENTIFIERS WHICH BEGIN WITH THE LETTER "D" OR "E" CORRESPOND TO THE A SUBUNIT. TURN IDENTIFIERS WHICH BEGIN WITH THE LETTER "B" OR "C" CORRESPOND TO THE B SUBUNIT. TURN IDENTIFIERS WHICH BEGIN WITH THE LETTER "G" OR "H" CORRESPOND TO THE G SUBUNIT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG400011
225 mM11Li2SO4
350 mM11NH4OAc
425 mMMOPS11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 103751 / % possible obs: 92 % / Rmerge(I) obs: 0.094

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→5 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.17 -
obs0.17 93453
Refinement stepCycle: LAST / Resolution: 2.2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21270 0 4 2585 23859
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.9

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