HEADER METAL BINDING PROTEIN 25-MAY-20 6Z4R TITLE SPERM WHALE MYOGLOBIN MUTANT (H64V V64A) BEARING THE NON-CANONICAL TITLE 2 AMINO ACID 3-THIENYLALANINE AS AXIAL HEME LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER MACROCEPHALUS; SOURCE 3 ORGANISM_COMMON: SPERM WHALE; SOURCE 4 ORGANISM_TAXID: 9755; SOURCE 5 GENE: MB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS GLOBIN, HEME PROTEIN, ENZYME, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.TINZL,D.HILVERT,P.R.E.MITTL REVDAT 4 24-JAN-24 6Z4R 1 REMARK REVDAT 3 13-SEP-23 6Z4R 1 SEQRES HETNAM HETSYN LINK REVDAT 3 2 1 ATOM REVDAT 2 30-JUN-21 6Z4R 1 JRNL REVDAT 1 28-APR-21 6Z4R 0 JRNL AUTH M.POTT,M.TINZL,T.HAYASHI,Y.OTA,D.DUNKELMANN,P.R.E.MITTL, JRNL AUTH 2 D.HILVERT JRNL TITL NONCANONICAL HEME LIGANDS STEER CARBENE TRANSFER REACTIVITY JRNL TITL 2 IN AN ARTIFICIAL METALLOENZYME*. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 60 15063 2021 JRNL REFN ESSN 1521-3773 JRNL PMID 33880851 JRNL DOI 10.1002/ANIE.202103437 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 19966 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 990 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 40.1600 - 3.7400 1.00 2735 139 0.1842 0.2517 REMARK 3 2 3.7400 - 2.9700 1.00 2727 138 0.1827 0.2003 REMARK 3 3 2.9700 - 2.6000 1.00 2729 145 0.2056 0.2610 REMARK 3 4 2.6000 - 2.3600 1.00 2708 143 0.2280 0.2903 REMARK 3 5 2.3600 - 2.1900 0.98 2682 141 0.2987 0.3291 REMARK 3 6 2.1900 - 2.0600 0.99 2716 143 0.3122 0.3510 REMARK 3 7 2.0600 - 1.9600 0.98 2679 141 0.3498 0.3801 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.517 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.31 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 : 0.014 1293 REMARK 3 ANGLE : 1.087 1751 REMARK 3 CHIRALITY : 0.041 183 REMARK 3 PLANARITY : 0.005 215 REMARK 3 DIHEDRAL : 19.810 472 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 6Z4R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292108919. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8-7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000031 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20069 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.770 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.16_3549 REMARK 200 STARTING MODEL: 6G5T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SPG BUFFER 28-32% PEG 1500 180 REMARK 280 NL PROTEIN 10 MG/ML + 20 NL SEED 100 NL WELL SOLUTION, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 20.03150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.10650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.63000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.10650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.03150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.63000 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 TOTAL BURIED SURFACE AREA: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL 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: 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 Q78 A 93 O - C - N 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 ASP A 20 78.88 -161.23 REMARK 500 PHE A 123 59.98 -152.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 Q78 A 93 20.44 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 HEM A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 337 O REMARK 620 2 HEM A 201 NA 109.0 REMARK 620 3 HEM A 201 NB 107.5 90.1 REMARK 620 4 HEM A 201 NC 85.2 164.9 90.4 REMARK 620 5 HEM A 201 ND 88.4 89.8 163.2 85.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues Q78 A 93 REMARK 800 through ALA A 94 bound to SER A 92 DBREF 6Z4R A 1 153 UNP P02185 MYG_PHYMC 2 154 SEQADV 6Z4R VAL A 64 UNP P02185 HIS 65 ENGINEERED MUTATION SEQADV 6Z4R ALA A 68 UNP P02185 VAL 69 ENGINEERED MUTATION SEQADV 6Z4R Q78 A 93 UNP P02185 HIS 94 ENGINEERED MUTATION SEQADV 6Z4R ALA A 154 UNP P02185 EXPRESSION TAG SEQRES 1 A 154 VAL LEU SER GLU GLY GLU TRP GLN LEU VAL LEU HIS VAL SEQRES 2 A 154 TRP ALA LYS VAL GLU ALA ASP VAL ALA GLY HIS GLY GLN SEQRES 3 A 154 ASP ILE LEU ILE ARG LEU PHE LYS SER HIS PRO GLU THR SEQRES 4 A 154 LEU GLU LYS PHE ASP ARG PHE LYS HIS LEU LYS THR GLU SEQRES 5 A 154 ALA GLU MET LYS ALA SER GLU ASP LEU LYS LYS VAL GLY SEQRES 6 A 154 VAL THR ALA LEU THR ALA LEU GLY ALA ILE LEU LYS LYS SEQRES 7 A 154 LYS GLY HIS HIS GLU ALA GLU LEU LYS PRO LEU ALA GLN SEQRES 8 A 154 SER Q78 ALA THR LYS HIS LYS ILE PRO ILE LYS TYR LEU SEQRES 9 A 154 GLU PHE ILE SER GLU ALA ILE ILE HIS VAL LEU HIS SER SEQRES 10 A 154 ARG HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY ALA SEQRES 11 A 154 MET ASN LYS ALA LEU GLU LEU PHE ARG LYS ASP ILE ALA SEQRES 12 A 154 ALA LYS TYR LYS GLU LEU GLY TYR GLN GLY ALA HET Q78 A 93 10 HET HEM A 201 43 HETNAM Q78 L-3-THIENYLALANINE HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN Q78 (2S)-2-AZANYL-3-THIOPHEN-3-YL-PROPANOIC ACID; 3-(3- HETSYN 2 Q78 THIENYL)-L-ALANINE HETSYN HEM HEME FORMUL 1 Q78 C7 H9 N O2 S FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *63(H2 O) HELIX 1 AA1 SER A 3 ALA A 19 1 17 HELIX 2 AA2 ASP A 20 HIS A 36 1 17 HELIX 3 AA3 PRO A 37 LYS A 47 5 11 HELIX 4 AA4 THR A 51 ALA A 57 1 7 HELIX 5 AA5 SER A 58 LYS A 78 1 21 HELIX 6 AA6 HIS A 82 LYS A 96 1 15 HELIX 7 AA7 PRO A 100 HIS A 119 1 20 HELIX 8 AA8 PRO A 120 PHE A 123 5 4 HELIX 9 AA9 GLY A 124 GLY A 150 1 27 LINK C SER A 92 N Q78 A 93 1555 1555 1.33 LINK C Q78 A 93 N ALA A 94 1555 1555 1.33 LINK FE HEM A 201 O HOH A 337 1555 1555 2.49 SITE 1 AC1 15 THR A 39 LYS A 42 PHE A 43 ARG A 45 SITE 2 AC1 15 THR A 67 ALA A 68 ALA A 71 LEU A 89 SITE 3 AC1 15 SER A 92 Q78 A 93 HIS A 97 ILE A 99 SITE 4 AC1 15 TYR A 103 HOH A 303 HOH A 337 SITE 1 AC2 11 LEU A 89 ALA A 90 GLN A 91 SER A 92 SITE 2 AC2 11 THR A 95 LYS A 96 LYS A 98 ILE A 99 SITE 3 AC2 11 TYR A 146 TYR A 151 HEM A 201 CRYST1 40.063 47.260 76.213 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 0.024961 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021160 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013121 0.00000