HEADER ELECTRON TRANSPORT 12-OCT-23 8WQZ TITLE X-RAY CRYSTAL STRUCTURE OF PSEUDOAZURIN MET16GLY VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSEUDOAZURIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BLUE COPPER PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACHROMOBACTER CYCLOCLASTES; SOURCE 3 ORGANISM_TAXID: 223; SOURCE 4 GENE: BCP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CU BINDING PROTEIN, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.SUGAI,T.YAMAGUCHI,T.KOHZUMA REVDAT 1 16-OCT-24 8WQZ 0 SPRSDE 16-OCT-24 8WQZ 5WV4 JRNL AUTH A.SUGAI,T.YAMAGUCHI,T.KOHZUMA JRNL TITL X-RAY CRYSTAL STRUCTURE OF PSEUDOAZURIN MET16GLY VARIANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 31296 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.153 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.007 REMARK 3 FREE R VALUE TEST SET COUNT : 1567 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2152 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.1970 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.2170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 909 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 159 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.82200 REMARK 3 B22 (A**2) : -0.20100 REMARK 3 B33 (A**2) : -0.62000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.039 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.037 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.021 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.006 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1018 ; 0.013 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 994 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1382 ; 1.986 ; 1.835 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2316 ; 0.616 ; 1.769 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 141 ; 6.721 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 2 ; 5.205 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 175 ;12.220 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 150 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1199 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 201 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 173 ; 0.268 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 66 ; 0.286 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 470 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 108 ; 0.221 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.151 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 534 ; 3.792 ; 0.952 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 534 ; 3.784 ; 0.952 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 679 ; 5.652 ; 1.719 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 680 ; 5.652 ; 1.719 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 484 ; 5.088 ; 1.184 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 485 ; 5.084 ; 1.186 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 701 ; 7.297 ; 2.037 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 702 ; 7.292 ; 2.039 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2012 ; 3.865 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8WQZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1300041768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999870 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31352 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 39.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 6.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 39.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.05600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 29.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.9.02 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 42 %(W/V) PEG200, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 15.59050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.55700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.50700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.55700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.59050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.50700 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 CG2 THR A 44 O HOH A 360 1.56 REMARK 500 O1 PEG A 202 O HOH A 302 1.81 REMARK 500 OD2 ASP A 116 O HOH A 303 2.16 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 ARG A 114 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES 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 201 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 40 ND1 REMARK 620 2 CYS A 78 SG 135.2 REMARK 620 3 HIS A 81 ND1 100.3 106.7 REMARK 620 4 MET A 86 SD 88.9 111.0 113.8 REMARK 620 N 1 2 3 DBREF 8WQZ A 1 124 UNP P19567 AZUP_ACHCY 29 152 SEQADV 8WQZ GLY A 16 UNP P19567 MET 44 VARIANT SEQRES 1 A 124 ALA ASP PHE GLU VAL HIS MET LEU ASN LYS GLY LYS ASP SEQRES 2 A 124 GLY ALA GLY VAL PHE GLU PRO ALA SER LEU LYS VAL ALA SEQRES 3 A 124 PRO GLY ASP THR VAL THR PHE ILE PRO THR ASP LYS GLY SEQRES 4 A 124 HIS ASN VAL GLU THR ILE LYS GLY MET ILE PRO ASP GLY SEQRES 5 A 124 ALA GLU ALA PHE LYS SER LYS ILE ASN GLU ASN TYR LYS SEQRES 6 A 124 VAL THR PHE THR ALA PRO GLY VAL TYR GLY VAL LYS CYS SEQRES 7 A 124 THR PRO HIS TYR GLY MET GLY MET VAL GLY VAL VAL GLN SEQRES 8 A 124 VAL GLY ASP ALA PRO ALA ASN LEU GLU ALA VAL LYS GLY SEQRES 9 A 124 ALA LYS ASN PRO LYS LYS ALA GLN GLU ARG LEU ASP ALA SEQRES 10 A 124 ALA LEU ALA ALA LEU GLY ASN HET CU A 201 1 HET PEG A 202 7 HET PEG A 203 7 HETNAM CU COPPER (II) ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 CU CU 2+ FORMUL 3 PEG 2(C4 H10 O3) FORMUL 5 HOH *159(H2 O) HELIX 1 AA1 HIS A 81 GLY A 85 5 5 HELIX 2 AA2 ASN A 98 GLY A 104 1 7 HELIX 3 AA3 PRO A 108 ALA A 121 1 14 SHEET 1 AA1 4 VAL A 17 GLU A 19 0 SHEET 2 AA1 4 ASP A 2 LEU A 8 -1 N HIS A 6 O GLU A 19 SHEET 3 AA1 4 ASP A 29 ILE A 34 1 O THR A 32 N VAL A 5 SHEET 4 AA1 4 TYR A 64 PHE A 68 -1 O TYR A 64 N PHE A 33 SHEET 1 AA2 4 SER A 22 VAL A 25 0 SHEET 2 AA2 4 VAL A 87 VAL A 92 1 O GLN A 91 N VAL A 25 SHEET 3 AA2 4 GLY A 72 LYS A 77 -1 N GLY A 72 O VAL A 92 SHEET 4 AA2 4 GLU A 43 THR A 44 -1 N GLU A 43 O LYS A 77 LINK ND1 HIS A 40 CU CU A 201 1555 1555 2.00 LINK SG CYS A 78 CU CU A 201 1555 1555 2.20 LINK ND1 HIS A 81 CU CU A 201 1555 1555 2.04 LINK SD MET A 86 CU CU A 201 1555 1555 2.52 CISPEP 1 GLU A 19 PRO A 20 0 -5.76 CRYST1 31.181 53.014 59.114 90.00 90.00 90.00 P 21 21 21 4 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 0.032071 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018863 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016916 0.00000