HEADER ELECTRON TRANSPORT 30-OCT-25 9YZ6 TITLE PSEUDOMONAS AERUGINOSA AZURIN MUTANT - M121H COMPND MOL_ID: 1; COMPND 2 MOLECULE: AZURIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: AZU, PA4922; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ELECTRON TRANSPORT PROTEIN, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.XU,Y.LU REVDAT 1 09-SEP-26 9YZ6 0 JRNL AUTH J.XU,L.YU,S.S.YU,Y.LIU,J.X.WANG,J.J.LI,C.VAN STAPPEN,H.Q.YU, JRNL AUTH 2 M.J.NILGES,Y.LU JRNL TITL STRUCTURAL BASIS FOR ORGANISM-DEPENDENT EFFECTS ON JRNL TITL 2 SPECTROSCOPIC PROPERTIES OF TYPE 1 COPPER AZURIN BY THE SAME JRNL TITL 3 AXIAL METHIONINE TO HISTIDINE MUTATION. JRNL REF J.INORG.BIOCHEM. V. 277 13209 2026 JRNL REFN ISSN 0162-0134 JRNL PMID 41518912 JRNL DOI 10.1016/J.JINORGBIO.2025.113209 REMARK 2 REMARK 2 RESOLUTION. 2.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 5553 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.281 REMARK 3 R VALUE (WORKING SET) : 0.278 REMARK 3 FREE R VALUE : 0.340 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 513 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 51.5900 - 3.9200 1.00 2444 124 0.2195 0.2799 REMARK 3 2 3.9200 - 3.1100 1.00 2435 122 0.3258 0.3831 REMARK 3 3 3.1100 - 2.7200 0.99 2410 122 0.3144 0.3800 REMARK 3 4 2.7200 - 2.4700 0.99 2439 145 0.3924 0.4222 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.213 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.213 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.60 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 987 REMARK 3 ANGLE : 0.944 1335 REMARK 3 CHIRALITY : 0.047 151 REMARK 3 PLANARITY : 0.005 175 REMARK 3 DIHEDRAL : 7.007 131 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9YZ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1000301609. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-SEP-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5566 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.470 REMARK 200 RESOLUTION RANGE LOW (A) : 51.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : 0.29030 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 74.3200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 11.70 REMARK 200 R MERGE FOR SHELL (I) : 0.55300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.520 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3 UL OF 20 MG PER ML APO-M121HAZ-PA IN REMARK 280 NAOAC (100 MM, PH 5.6) WERE MIXED WITH VARIOUS VOLUMES OF WELL REMARK 280 BUFFER (3 UL, 2 UL, AND 1 UL) ON A SILICA SLIDE AND ALLOWED TO REMARK 280 EQUILIBRATE OVER 300 UL WELL BUFFER. (25% PEG 4000, 100 MM LINO3 REMARK 280 , 10 MM CUSO4 , AND 100 MM TRIS PH 8.0), VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.58850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.58850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 24.78350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.90950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.78350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.90950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.58850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.78350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 28.90950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.58850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.78350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 28.90950 REMARK 290 SMTRY3 8 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 24 CD CE NZ REMARK 470 LYS A 122 CG CD CE NZ 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 MET A 13 CA - CB - CG ANGL. DEV. = 10.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 2 137.44 60.54 REMARK 500 ASP A 11 28.45 -75.85 REMARK 500 GLN A 12 29.99 -142.26 REMARK 500 MET A 13 76.62 35.11 REMARK 500 ASP A 69 10.22 -69.76 REMARK 500 PRO A 115 114.20 -38.82 REMARK 500 HIS A 117 -58.41 53.84 REMARK 500 LEU A 120 -71.63 -109.60 REMARK 500 LYS A 122 -154.82 -125.85 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 202 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 2 OE2 REMARK 620 2 HIS A 83 NE2 105.8 REMARK 620 3 HOH A 302 O 105.2 60.1 REMARK 620 N 1 2 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 46 ND1 REMARK 620 2 CYS A 112 SG 112.4 REMARK 620 3 HIS A 117 ND1 110.2 116.8 REMARK 620 4 HIS A 121 NE2 104.1 115.8 95.8 REMARK 620 N 1 2 3 DBREF 9YZ6 A 1 128 UNP P00282 AZUR_PSEAE 21 148 SEQADV 9YZ6 HIS A 121 UNP P00282 MET 141 ENGINEERED MUTATION SEQRES 1 A 128 ALA GLU CYS SER VAL ASP ILE GLN GLY ASN ASP GLN MET SEQRES 2 A 128 GLN PHE ASN THR ASN ALA ILE THR VAL ASP LYS SER CYS SEQRES 3 A 128 LYS GLN PHE THR VAL ASN LEU SER HIS PRO GLY ASN LEU SEQRES 4 A 128 PRO LYS ASN VAL MET GLY HIS ASN TRP VAL LEU SER THR SEQRES 5 A 128 ALA ALA ASP MET GLN GLY VAL VAL THR ASP GLY MET ALA SEQRES 6 A 128 SER GLY LEU ASP LYS ASP TYR LEU LYS PRO ASP ASP SER SEQRES 7 A 128 ARG VAL ILE ALA HIS THR LYS LEU ILE GLY SER GLY GLU SEQRES 8 A 128 LYS ASP SER VAL THR PHE ASP VAL SER LYS LEU LYS GLU SEQRES 9 A 128 GLY GLU GLN TYR MET PHE PHE CYS THR PHE PRO GLY HIS SEQRES 10 A 128 SER ALA LEU HIS LYS GLY THR LEU THR LEU LYS HET CU A 201 1 HET CU A 202 1 HETNAM CU COPPER (II) ION FORMUL 2 CU 2(CU 2+) FORMUL 4 HOH *2(H2 O) HELIX 1 AA1 ASP A 55 SER A 66 1 12 HELIX 2 AA2 GLY A 67 ASP A 71 5 5 HELIX 3 AA3 SER A 100 LEU A 102 5 3 SHEET 1 AA1 3 SER A 4 GLN A 8 0 SHEET 2 AA1 3 GLN A 28 SER A 34 1 O ASN A 32 N ILE A 7 SHEET 3 AA1 3 ASP A 93 ASP A 98 -1 O ASP A 93 N LEU A 33 SHEET 1 AA2 5 ALA A 19 ASP A 23 0 SHEET 2 AA2 5 LYS A 122 LYS A 128 1 O THR A 126 N ILE A 20 SHEET 3 AA2 5 TYR A 108 PHE A 111 -1 N PHE A 110 O GLY A 123 SHEET 4 AA2 5 VAL A 49 THR A 52 -1 N SER A 51 O MET A 109 SHEET 5 AA2 5 ALA A 82 HIS A 83 -1 O ALA A 82 N LEU A 50 SSBOND 1 CYS A 3 CYS A 26 1555 1555 2.04 LINK OE2 GLU A 2 CU CU A 202 1555 1555 2.09 LINK ND1 HIS A 46 CU CU A 201 1555 1555 2.09 LINK NE2 HIS A 83 CU CU A 202 1555 8455 2.35 LINK SG CYS A 112 CU CU A 201 1555 1555 2.41 LINK ND1 HIS A 117 CU CU A 201 1555 1555 2.23 LINK NE2 HIS A 121 CU CU A 201 1555 1555 2.32 LINK CU CU A 202 O HOH A 302 1555 1555 2.27 CRYST1 49.567 57.819 103.177 90.00 90.00 90.00 C 2 2 21 8 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 0.020175 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017295 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009692 0.00000 CONECT 14 972 CONECT 20 191 CONECT 191 20 CONECT 343 971 CONECT 852 971 CONECT 888 971 CONECT 920 971 CONECT 971 343 852 888 920 CONECT 972 14 974 CONECT 974 972 MASTER 284 0 2 3 8 0 0 6 973 1 10 10 END