HEADER HEME-BINDING PROTEIN 23-FEB-18 6CII TITLE CRYSTAL STRUCTURE OF CHLAMYDOMONAS REINHARDTII THB1 IN THE CYANOMET TITLE 2 STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHLAMYDOMONAS REINHARDTII THB1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRUNCATED HEMOGLOBIN 1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHLAMYDOMONAS REINHARDTII; SOURCE 3 ORGANISM_COMMON: CHLAMYDOMONAS SMITHII; SOURCE 4 ORGANISM_TAXID: 3055; SOURCE 5 GENE: THB1, CHLREDRAFT_81856; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HEME-BINDING PROTEIN, HEME, GLOBIN, TRUNCATED HEMOGLOBIN, 2-ON-2 KEYWDS 2 HEMOGLOBIN, CYANIDE, CYANOMET EXPDTA X-RAY DIFFRACTION AUTHOR J.E.MARTINEZ,J.L.SCHLESSMAN,J.T.J.LECOMTE REVDAT 4 13-MAR-24 6CII 1 REMARK REVDAT 3 28-APR-21 6CII 1 JRNL REVDAT 2 27-NOV-19 6CII 1 REMARK REVDAT 1 25-APR-18 6CII 0 JRNL AUTH J.E.MARTINEZ,J.L.SCHLESSMAN,J.T.J.LECOMTE JRNL TITL CONTROL OF DISTAL LYSINE COORDINATION IN A MONOMERIC JRNL TITL 2 HEMOGLOBIN: A ROLE FOR HEME PERIPHERAL INTERACTIONS JRNL REF J.INORG.BIOCHEM. V. 219 11437 2021 JRNL REFN ISSN 0162-0134 JRNL DOI 10.1016/J.JINORGBIO.2021.111437 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13RC1_2954: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 27344 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 2722 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 21.5035 - 4.5229 1.00 1306 142 0.1761 0.1637 REMARK 3 2 4.5229 - 3.5954 1.00 1304 141 0.1427 0.1559 REMARK 3 3 3.5954 - 3.1425 1.00 1297 139 0.1608 0.1696 REMARK 3 4 3.1425 - 2.8559 1.00 1281 146 0.1639 0.1911 REMARK 3 5 2.8559 - 2.6516 1.00 1298 145 0.1731 0.1811 REMARK 3 6 2.6516 - 2.4955 1.00 1301 146 0.1585 0.1953 REMARK 3 7 2.4955 - 2.3707 1.00 1292 141 0.1596 0.1809 REMARK 3 8 2.3707 - 2.2676 1.00 1312 146 0.1599 0.2170 REMARK 3 9 2.2676 - 2.1804 1.00 1259 142 0.1579 0.1879 REMARK 3 10 2.1804 - 2.1053 1.00 1312 147 0.1697 0.2095 REMARK 3 11 2.1053 - 2.0395 1.00 1293 148 0.1680 0.2462 REMARK 3 12 2.0395 - 1.9812 1.00 1300 143 0.1724 0.2380 REMARK 3 13 1.9812 - 1.9291 1.00 1298 139 0.1598 0.2120 REMARK 3 14 1.9291 - 1.8821 1.00 1308 142 0.1704 0.1813 REMARK 3 15 1.8821 - 1.8393 1.00 1272 143 0.1551 0.2236 REMARK 3 16 1.8393 - 1.8002 1.00 1306 143 0.1557 0.2059 REMARK 3 17 1.8002 - 1.7642 1.00 1295 141 0.1653 0.2253 REMARK 3 18 1.7642 - 1.7309 1.00 1301 146 0.1776 0.1996 REMARK 3 19 1.7309 - 1.7000 1.00 1287 142 0.1917 0.2682 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.18 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 : 0.010 1083 REMARK 3 ANGLE : 1.103 1482 REMARK 3 CHIRALITY : 0.057 149 REMARK 3 PLANARITY : 0.006 194 REMARK 3 DIHEDRAL : 15.572 407 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 6CII COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232663. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER 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 : CCD REMARK 200 DETECTOR MANUFACTURER : AGILENT ATLAS CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO 1.171.36.32 REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO 1.171.36.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27344 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 21.502 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.19200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.880 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX 1.13RC1_2954 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5, 30% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 2 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 60.63850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.31925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 90.95775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 60.63850 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 90.95775 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 30.31925 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 330 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 405 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 428 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 ASP A 4 REMARK 465 THR A 5 REMARK 465 GLY A 130 REMARK 465 GLU A 131 REMARK 465 ALA A 132 REMARK 465 GLY A 133 REMARK 465 ALA A 134 REMARK 465 ALA A 135 REMARK 465 ASN A 136 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 FE HEM A 201 C CYN A 202 2.03 REMARK 500 OH TYR A 68 O HOH A 301 2.06 REMARK 500 OH TYR A 68 O HOH A 302 2.09 REMARK 500 OE1 GLU A 114 O HOH A 303 2.19 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 HIS A 77 NE2 REMARK 620 2 HEM A 201 NA 86.6 REMARK 620 3 HEM A 201 NB 88.8 90.8 REMARK 620 4 HEM A 201 NC 94.1 178.6 88.0 REMARK 620 5 HEM A 201 ND 91.0 91.2 178.0 90.0 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 residue CYN A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XDI RELATED DB: PDB REMARK 900 4XDI CONTAINS NO CYANIDE LIGAND DBREF 6CII A 2 136 UNP A8JAR4 A8JAR4_CHLRE 2 136 SEQRES 1 A 135 ALA ALA ASP THR ALA PRO ALA ASP SER LEU TYR SER ARG SEQRES 2 A 135 MET GLY GLY GLU ALA ALA VAL GLU LYS ALA VAL ASP VAL SEQRES 3 A 135 PHE TYR GLU ARG ILE VAL ALA ASP PRO GLN LEU ALA PRO SEQRES 4 A 135 PHE PHE ALA ASN VAL ASP MET LYS LYS GLN ARG ARG LYS SEQRES 5 A 135 GLN VAL ALA PHE MET THR TYR VAL PHE GLY GLY SER GLY SEQRES 6 A 135 ALA TYR GLU GLY ARG ASP LEU GLY ALA SER HIS ARG ARG SEQRES 7 A 135 LEU ILE ARG GLU GLN GLY MET ASN HIS HIS HIS PHE ASP SEQRES 8 A 135 LEU VAL ALA ALA HIS LEU ASP SER THR LEU GLN GLU LEU SEQRES 9 A 135 GLY VAL ALA GLN GLU LEU LYS ALA GLU ALA MET ALA ILE SEQRES 10 A 135 VAL ALA SER ALA ARG PRO LEU ILE PHE GLY THR GLY GLU SEQRES 11 A 135 ALA GLY ALA ALA ASN HET HEM A 201 43 HET CYN A 202 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CYN CYANIDE ION HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 CYN C N 1- FORMUL 4 HOH *140(H2 O) HELIX 1 AA1 ALA A 6 ASP A 9 5 4 HELIX 2 AA2 SER A 10 MET A 15 1 6 HELIX 3 AA3 GLY A 16 ASP A 35 1 20 HELIX 4 AA4 LEU A 38 ALA A 43 1 6 HELIX 5 AA5 ASP A 46 PHE A 62 1 17 HELIX 6 AA6 ASP A 72 GLN A 84 1 13 HELIX 7 AA7 ASN A 87 LEU A 105 1 19 HELIX 8 AA8 ALA A 108 GLY A 128 1 21 LINK NE2 HIS A 77 FE HEM A 201 1555 1555 2.06 SITE 1 AC1 23 LEU A 38 PHE A 41 PHE A 42 ASN A 44 SITE 2 AC1 23 GLN A 50 LYS A 53 GLN A 54 PHE A 57 SITE 3 AC1 23 ARG A 71 SER A 76 HIS A 77 ARG A 79 SITE 4 AC1 23 LEU A 80 MET A 86 HIS A 90 PHE A 91 SITE 5 AC1 23 VAL A 94 ILE A 126 CYN A 202 HOH A 301 SITE 6 AC1 23 HOH A 310 HOH A 339 HOH A 392 SITE 1 AC2 4 TYR A 29 GLN A 50 GLN A 54 HEM A 201 CRYST1 45.992 45.992 121.277 90.00 90.00 90.00 P 41 2 2 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 0.021743 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021743 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008246 0.00000