HEADER ELECTRON TRANSPORT 21-JUN-07 2QDW TITLE STRUCTURE OF CU(I) FORM OF THE M51A MUTANT OF AMICYANIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMICYANIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARACOCCUS DENITRIFICANS; SOURCE 3 ORGANISM_TAXID: 266; SOURCE 4 GENE: MAUC, AMI; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMEG201 KEYWDS BETA BARREL, CUPREDOXIN, ELECTRON TRANSFER, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.K.MA,Y.WANG,C.J.CARRELL,F.S.MATHEWS,V.L.DAVIDSON REVDAT 5 30-AUG-23 2QDW 1 REMARK REVDAT 4 20-OCT-21 2QDW 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2QDW 1 VERSN REVDAT 2 15-APR-08 2QDW 1 CONECT LINK MASTER SITE REVDAT 2 2 1 REMARK REVDAT 1 11-DEC-07 2QDW 0 JRNL AUTH J.K.MA,Y.WANG,C.J.CARRELL,F.S.MATHEWS,V.L.DAVIDSON JRNL TITL A SINGLE METHIONINE RESIDUE DICTATES THE KINETIC MECHANISM JRNL TITL 2 OF INTERPROTEIN ELECTRON TRANSFER FROM METHYLAMINE JRNL TITL 3 DEHYDROGENASE TO AMICYANIN. JRNL REF BIOCHEMISTRY V. 46 11137 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17824674 JRNL DOI 10.1021/BI7012307 REMARK 2 REMARK 2 RESOLUTION. 0.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.122 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.121 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2622 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 52498 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.119 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.118 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.144 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2466 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 49419 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 813 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 954.25 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 785.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 7 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 8793 REMARK 3 NUMBER OF RESTRAINTS : 10751 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 ANGLE DISTANCES (A) : 0.039 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.032 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.106 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.110 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.059 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.050 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.092 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) REMARK 4 REMARK 4 2QDW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043475. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90000 REMARK 200 MONOCHROMATOR : GE(111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52498 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.920 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 45.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.25900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: PDB CODE 1AAC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5-3.0 M PHOSPHATE 10 MG/ML REMARK 280 AMICYANIN, PH 5.5, EVAPORATION, TEMPERATURE 293K 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 27.68000 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 1116 O HOH A 1200 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 27 C MET A 28 N 0.286 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 1 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 GLU A 8 OE1 - CD - OE2 ANGL. DEV. = -9.8 DEGREES REMARK 500 MET A 71 CG - SD - CE ANGL. DEV. = 16.7 DEGREES REMARK 500 MET A 72 CG - SD - CE ANGL. DEV. = -15.5 DEGREES REMARK 500 GLU A 75 OE1 - CD - OE2 ANGL. DEV. = -8.8 DEGREES REMARK 500 ASP A 89 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 PHE A 97 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU1 A 1107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QDV RELATED DB: PDB DBREF 2QDW A 1 105 UNP P22364 AMCY_PARDE 27 131 SEQADV 2QDW ALA A 51 UNP P22364 MET 77 ENGINEERED MUTATION SEQRES 1 A 105 ASP LYS ALA THR ILE PRO SER GLU SER PRO PHE ALA ALA SEQRES 2 A 105 ALA GLU VAL ALA ASP GLY ALA ILE VAL VAL ASP ILE ALA SEQRES 3 A 105 LYS MHO LYS TYR GLU THR PRO GLU LEU HIS VAL LYS VAL SEQRES 4 A 105 GLY ASP THR VAL THR TRP ILE ASN ARG GLU ALA ALA PRO SEQRES 5 A 105 HIS ASN VAL HIS PHE VAL ALA GLY VAL LEU GLY GLU ALA SEQRES 6 A 105 ALA LEU LYS GLY PRO MET MET LYS LYS GLU GLN ALA TYR SEQRES 7 A 105 SER LEU THR PHE THR GLU ALA GLY THR TYR ASP TYR HIS SEQRES 8 A 105 CYS THR PRO HIS PRO PHE MET ARG GLY LYS VAL VAL VAL SEQRES 9 A 105 GLU MODRES 2QDW MHO A 28 MET S-OXYMETHIONINE HET MHO A 28 9 HET CU1 A1107 2 HET PO4 A 201 5 HET PO4 A 202 5 HETNAM MHO S-OXYMETHIONINE HETNAM CU1 COPPER (I) ION HETNAM PO4 PHOSPHATE ION FORMUL 1 MHO C5 H11 N O3 S FORMUL 2 CU1 CU 1+ FORMUL 3 PO4 2(O4 P 3-) FORMUL 5 HOH *139(H2 O) HELIX 1 1 ALA A 14 VAL A 16 5 3 SHEET 1 A 3 ALA A 3 THR A 4 0 SHEET 2 A 3 GLN A 76 PHE A 82 -1 O THR A 81 N THR A 4 SHEET 3 A 3 PHE A 11 ALA A 12 -1 N PHE A 11 O ALA A 77 SHEET 1 B 5 ALA A 3 THR A 4 0 SHEET 2 B 5 GLN A 76 PHE A 82 -1 O THR A 81 N THR A 4 SHEET 3 B 5 THR A 42 ASN A 47 -1 N VAL A 43 O LEU A 80 SHEET 4 B 5 ILE A 21 ALA A 26 1 N ILE A 21 O THR A 42 SHEET 5 B 5 LYS A 29 TYR A 30 -1 O LYS A 29 N ALA A 26 SHEET 1 C 3 GLU A 34 VAL A 37 0 SHEET 2 C 3 ARG A 99 VAL A 104 1 O VAL A 103 N LEU A 35 SHEET 3 C 3 GLY A 86 HIS A 91 -1 N GLY A 86 O VAL A 104 SHEET 1 D 2 HIS A 56 PHE A 57 0 SHEET 2 D 2 LEU A 67 LYS A 68 -1 O LEU A 67 N PHE A 57 LINK C LYS A 27 N AMHO A 28 1555 1555 1.33 LINK C AMHO A 28 N LYS A 29 1555 1555 1.32 LINK ND1 HIS A 53 CU BCU1 A1107 1555 1555 1.99 LINK ND1 HIS A 53 CU ACU1 A1107 1555 1555 2.03 SITE 1 AC1 4 HIS A 53 CYS A 92 HIS A 95 MET A 98 SITE 1 AC2 4 ASP A 1 LYS A 2 GLY A 63 GLU A 64 SITE 1 AC3 6 LYS A 27 LYS A 29 GLU A 31 HOH A1193 SITE 2 AC3 6 HOH A1200 HOH A1202 CRYST1 28.210 55.360 27.270 90.00 95.75 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 0.035448 0.000000 0.003569 0.00000 SCALE2 0.000000 0.018064 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036856 0.00000