PDB Short entry for 1CUO HEADER ELECTRON TRANSPORT 21-AUG-99 1CUO TITLE CRYSTAL STRUCTURE ANALYSIS OF ISOMER-2 AZURIN FROM TITLE 2 METHYLOMONAS J COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (AZURIN ISO-2); COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLOMONAS SP. J; SOURCE 3 ORGANISM_TAXID: 32038 KEYWDS BETA BARREL, PERIPLASMIC, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR T.INOUE,N.NISHIO,Y.KAI,S.SUZUKI,K.KATAOKA REVDAT 3 24-FEB-09 1CUO 1 VERSN REVDAT 2 29-MAR-05 1CUO 1 JRNL REMARK MASTER REVDAT 1 23-AUG-00 1CUO 0 JRNL AUTH T.INOUE,S.SUZUKI,N.NISHIO,K.YAMAGUCHI,K.KATAOKA, JRNL AUTH 2 J.TOBARI,X.YONG,S.HAMANAKA,H.MATSUMURA,Y.KAI JRNL TITL THE SIGNIFICANCE OF THE FLEXIBLE LOOP IN THE JRNL TITL 2 AZURIN (AZ-ISO2) FROM THE OBLIGATE METHYLOTROPH JRNL TITL 3 METHYLOMONAS SP. STRAIN J. JRNL REF J.MOL.BIOL. V. 333 117 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 14516747 JRNL DOI 10.1016/J.JMB.2003.08.002 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.P.AMBLER,J.TOBARI REMARK 1 TITL TWO DISTINCT AZURINS FUNCTION IN THE REMARK 1 TITL 2 ELECTRON-TRANSPORT CHAIN OF THE OBLIGATE REMARK 1 TITL 3 METHYLOTROPH METHYLOMONAS J REMARK 1 REF BIOCHEM.J. V. 261 495 1989 REMARK 1 REFN ISSN 0264-6021 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.INOUE,N.NISHIO,Y.KAI,S.SUZUKI,K.KATAOKA REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY STUDY OF REMARK 1 TITL 2 ISO-2 AZURIN FROM THE METHYLOTROPHIC BACTERIUM, REMARK 1 TITL 3 METHYLOMONAS J REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 307 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444998014036 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 3 NUMBER OF REFLECTIONS : 11453 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 589 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 967 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.011 ; NULL REMARK 3 ANGLE DISTANCE (A) : 0.027 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CUO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-99. REMARK 100 THE RCSB ID CODE IS RCSB009552. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-97 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12059 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 19.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 0.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.19200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, SODIUM CACODYLATE, PH 5.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 16.83500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 MET A 13 48.47 -109.08 REMARK 500 MET A 44 38.81 -140.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 130 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 117 ND1 REMARK 620 2 HIS A 46 ND1 102.9 REMARK 620 3 CYS A 112 SG 115.7 137.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 130 DBREF 1CUO A 1 129 UNP P12335 AZUR2_METJ 1 129 SEQRES 1 A 129 ALA SER CYS GLU THR THR VAL THR SER GLY ASP THR MET SEQRES 2 A 129 THR TYR SER THR ARG SER ILE SER VAL PRO ALA SER CYS SEQRES 3 A 129 ALA GLU PHE THR VAL ASN PHE GLU HIS LYS GLY HIS MET SEQRES 4 A 129 PRO LYS THR GLY MET GLY HIS ASN TRP VAL LEU ALA LYS SEQRES 5 A 129 SER ALA ASP VAL GLY ASP VAL ALA LYS GLU GLY ALA HIS SEQRES 6 A 129 ALA GLY ALA ASP ASN ASN PHE VAL THR PRO GLY ASP LYS SEQRES 7 A 129 ARG VAL ILE ALA PHE THR PRO ILE ILE GLY GLY GLY GLU SEQRES 8 A 129 LYS THR SER VAL LYS PHE LYS VAL SER ALA LEU SER LYS SEQRES 9 A 129 ASP GLU ALA TYR THR TYR PHE CYS SER TYR PRO GLY HIS SEQRES 10 A 129 PHE SER MET MET ARG GLY THR LEU LYS LEU GLU GLU HET CU A 130 1 HETNAM CU COPPER (II) ION FORMUL 2 CU CU 2+ FORMUL 3 HOH *82(H2 O) HELIX 1 1 PRO A 40 GLY A 45 1 6 HELIX 2 2 ASP A 55 HIS A 65 1 11 HELIX 3 3 ALA A 66 ASN A 71 5 6 HELIX 4 4 SER A 100 LEU A 102 5 3 SHEET 1 A 3 GLU A 4 SER A 9 0 SHEET 2 A 3 GLU A 28 HIS A 35 1 O THR A 30 N THR A 5 SHEET 3 A 3 LYS A 92 LYS A 98 -1 O THR A 93 N PHE A 33 SHEET 1 B 5 SER A 19 PRO A 23 0 SHEET 2 B 5 ARG A 122 GLU A 128 1 O THR A 124 N ILE A 20 SHEET 3 B 5 TYR A 108 PHE A 111 -1 O TYR A 108 N LEU A 125 SHEET 4 B 5 VAL A 49 LYS A 52 -1 N VAL A 49 O PHE A 111 SHEET 5 B 5 ALA A 82 PHE A 83 -1 O ALA A 82 N LEU A 50 SSBOND 1 CYS A 3 CYS A 26 1555 1555 2.02 LINK CU CU A 130 ND1 HIS A 117 1555 1555 2.05 LINK CU CU A 130 ND1 HIS A 46 1555 1555 2.07 LINK CU CU A 130 SG CYS A 112 1555 1555 2.03 SITE 1 AC1 5 GLY A 45 HIS A 46 CYS A 112 HIS A 117 SITE 2 AC1 5 MET A 121 CRYST1 32.960 33.670 47.340 90.00 101.35 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.030340 0.000000 0.006090 0.00000 SCALE2 0.000000 0.029700 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021550 0.00000