HEADER OXYGEN STORAGE/TRANSPORT 20-FEB-04 1UX8 TITLE X-RAY STRUCTURE OF TRUNCATED OXYGEN-AVID HAEMOGLOBIN FROM TITLE 2 BACILLUS SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: YJBI PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRUNCATED HEMOGLOBIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS OXYGEN STORAGE/TRANSPORT, TRUNCATED HEMOGLOBIN, OXYGEN KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.ILARI,L.GIANGIACOMO,A.BOFFI,E.CHIANCONE REVDAT 3 24-FEB-09 1UX8 1 VERSN REVDAT 2 09-MAR-05 1UX8 1 JRNL REVDAT 1 07-DEC-04 1UX8 0 JRNL AUTH L.GIANGIACOMO,A.ILARI,A.BOFFI,V.MOREA,E.CHIANCONE JRNL TITL THE TRUNCATED OXYGEN-AVID HEMOGLOBIN FROM BACILLUS JRNL TITL 2 SUBTILIS: X-RAY STRUCTURE AND LIGAND BINDING JRNL TITL 3 PROPERTIES JRNL REF J.BIOL.CHEM. V. 280 9192 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15590662 JRNL DOI 10.1074/JBC.M407267200 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.5 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 6442 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.8 REMARK 3 FREE R VALUE TEST SET COUNT : 323 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 971 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 77 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.16 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UX8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-FEB-04. REMARK 100 THE PDBE ID CODE IS EBI-14609. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6975 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1NGK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.6 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.2 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2,0 M AMMONIUM SULFATE, REMARK 280 5% V/V ISOPROPANOL, PH=6.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 67.26850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.59650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.59650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.63425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.59650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.59650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 100.90275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.59650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.59650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.63425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.59650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.59650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 100.90275 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 0.00000 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 67.26850 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 GENERATING THE BIOMOLECULE 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: PQS 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 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 GLN A 3 REMARK 465 SER A 4 REMARK 465 PHE A 5 REMARK 465 THR A 125 REMARK 465 GLU A 126 REMARK 465 ALA A 127 REMARK 465 GLU A 128 REMARK 465 ASP A 129 REMARK 465 ARG A 130 REMARK 465 SER A 131 REMARK 465 SER A 132 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 GLN A 124 CA C O CB CG CD OE1 NE2 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 OE1 GLN A 51 - NE2 HIS A 67 2.15 REMARK 500 OD2 ASP A 95 - O HOH A 2061 1.96 REMARK 500 OE2 GLU A 103 - O HOH A 2065 2.14 REMARK 500 O HOH A 2036 - O HOH A 2042 2.17 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 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 65 -35.33 -34.34 REMARK 500 MET A 71 66.76 29.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): 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 700 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYN A1124 C REMARK 620 2 CYN A1124 N 1.6 REMARK 620 3 HEM A 700 NA 85.4 85.0 REMARK 620 4 HEM A 700 NB 98.8 97.3 88.7 REMARK 620 5 HEM A 700 ND 77.1 78.7 87.7 174.8 REMARK 620 6 HEM A 700 NC 90.6 91.0 175.9 91.7 91.6 REMARK 620 7 HIS A 76 NE2 169.1 170.7 97.4 91.8 92.4 86.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CYN A1124 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1125 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 700 DBREF 1UX8 A 1 132 UNP O31607 O31607 1 132 SEQRES 1 A 132 MET GLY GLN SER PHE ASN ALA PRO TYR GLU ALA ILE GLY SEQRES 2 A 132 GLU GLU LEU LEU SER GLN LEU VAL ASP THR PHE TYR GLU SEQRES 3 A 132 ARG VAL ALA SER HIS PRO LEU LEU LYS PRO ILE PHE PRO SEQRES 4 A 132 SER ASP LEU THR GLU THR ALA ARG LYS GLN LYS GLN PHE SEQRES 5 A 132 LEU THR GLN TYR LEU GLY GLY PRO PRO LEU TYR THR GLU SEQRES 6 A 132 GLU HIS GLY HIS PRO MET LEU ARG ALA ARG HIS LEU PRO SEQRES 7 A 132 PHE PRO ILE THR ASN GLU ARG ALA ASP ALA TRP LEU SER SEQRES 8 A 132 CYS MET LYS ASP ALA MET ASP HIS VAL GLY LEU GLU GLY SEQRES 9 A 132 GLU ILE ARG GLU PHE LEU PHE GLY ARG LEU GLU LEU THR SEQRES 10 A 132 ALA ARG HIS MET VAL ASN GLN THR GLU ALA GLU ASP ARG SEQRES 11 A 132 SER SER HET CYN A1124 2 HET CL A1125 1 HET HEM A 700 43 HETNAM CYN CYANIDE ION HETNAM CL CHLORIDE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM [DIHYDROGEN 3,7,12,17-TETRAMETHYL-8,13- HETSYN 2 HEM DIVINYL-2,18-PORPHINEDIPROPIONATO(2-)]IRON FORMUL 2 CYN C N 1- FORMUL 3 CL CL 1- FORMUL 4 HEM C34 H32 FE N4 O4 FORMUL 5 HOH *77(H2 O1) HELIX 1 1 ALA A 7 ALA A 11 5 5 HELIX 2 2 ILE A 12 HIS A 31 1 20 HELIX 3 3 LEU A 34 PHE A 38 5 5 HELIX 4 4 LEU A 42 LEU A 57 1 16 HELIX 5 5 PRO A 61 GLY A 68 1 8 HELIX 6 6 MET A 71 LEU A 77 1 7 HELIX 7 7 THR A 82 GLY A 101 1 20 HELIX 8 8 GLY A 104 VAL A 122 1 19 LINK NE2 HIS A 76 FE HEM A 700 1555 1555 1.91 LINK FE HEM A 700 C CYN A1124 1555 1555 1.92 LINK FE HEM A 700 N CYN A1124 1555 1555 3.09 SITE 1 AC1 4 TYR A 25 GLN A 49 TRP A 89 HEM A 700 SITE 1 AC2 1 HOH A2049 SITE 1 AC3 14 ILE A 37 PHE A 38 THR A 45 LYS A 48 SITE 2 AC3 14 GLN A 49 PHE A 52 LEU A 53 TYR A 63 SITE 3 AC3 14 ARG A 75 HIS A 76 ILE A 81 ALA A 86 SITE 4 AC3 14 TRP A 89 CYN A1124 CRYST1 41.193 41.193 134.537 90.00 90.00 90.00 P 41 21 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 0.024276 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024276 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007433 0.00000 MASTER 303 0 3 8 0 0 6 6 0 0 0 11 END