HEADER OXYGEN STORAGE/TRANSPORT 03-MAR-06 2DFO OBSLTE 09-MAY-06 2DFO 2DN1 TITLE 1.25A RESOLUTION CRSYTAL STRUCTURE OF HUMAN HEMOGLOBIN IN TITLE 2 THE OXY FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN ALPHA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HEMOGLOBIN ALPHA CHAIN, ALPHA-GLOBIN; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEMOGLOBIN BETA SUBUNIT; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: HEMOGLOBIN BETA CHAIN, BETA-GLOBIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 TISSUE: BLOOD, ERYTHROCYTE; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 TISSUE: BLOOD, ERYTHROCYTE KEYWDS HEMOGLOBIN, HIGH RESOLUTION, CRYSTAL STRUCTURE EXPDTA X-RAY DIFFRACTION AUTHOR S.-Y.PARK,T.YOKOYAMA,N.SHIBAYAMA,Y.SHIRO,R.H.T.TAME REVDAT 2 09-MAY-06 2DFO 1 OBSLTE REVDAT 1 21-MAR-06 2DFO 0 JRNL AUTH S.-Y.PARK,T.YOKOYAMA,N.SHIBAYAMA,Y.SHIRO,R.H.T.TAME JRNL TITL 1.25A RESOLUTION CRYSTAL STRUCTURE OF HUMAN JRNL TITL 2 HEMOGLOBIN IN THE OXY, DEOXY AND CARBON MONOXY JRNL TITL 3 FORMS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.183 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3684 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 69507 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2192 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 104 REMARK 3 SOLVENT ATOMS : 283 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.082 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.047 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.063 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.060 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.012 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.057 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DFO COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-2006. REMARK 100 THE RCSB ID CODE IS RCSB025363. 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 : 6.70 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73528 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: X-PLOR REMARK 200 STARTING MODEL: 1IRD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM PHOSPHATE, POTASSIUM REMARK 280 PHOSPHATE, TOLUENE, GLYCEROL, PH 6.7, BATCH, TEMPERATURE 277K 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,1/2+Z REMARK 290 3555 1/2-Y,1/2+X,1/4+Z REMARK 290 4555 1/2+Y,1/2-X,3/4+Z REMARK 290 5555 1/2-X,1/2+Y,1/4-Z REMARK 290 6555 1/2+X,1/2-Y,3/4-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,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 95.85450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.71750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.71750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.92725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.71750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.71750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 143.78175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.71750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.71750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.92725 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.71750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.71750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 143.78175 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 95.85450 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DFQ RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN THE DEOXY FORM DBREF 2DFO A 1 141 UNP P69905 HBA_HUMAN 1 141 DBREF 2DFO B 1 146 UNP P68871 HBB_HUMAN 1 146 SEQRES 1 A 141 VAL LEU SER PRO ALA ASP LYS THR ASN VAL LYS ALA ALA SEQRES 2 A 141 TRP GLY LYS VAL GLY ALA HIS ALA GLY GLU TYR GLY ALA SEQRES 3 A 141 GLU ALA LEU GLU ARG MET PHE LEU SER PHE PRO THR THR SEQRES 4 A 141 LYS THR TYR PHE PRO HIS PHE ASP LEU SER HIS GLY SER SEQRES 5 A 141 ALA GLN VAL LYS GLY HIS GLY LYS LYS VAL ALA ASP ALA SEQRES 6 A 141 LEU THR ASN ALA VAL ALA HIS VAL ASP ASP MET PRO ASN SEQRES 7 A 141 ALA LEU SER ALA LEU SER ASP LEU HIS ALA HIS LYS LEU SEQRES 8 A 141 ARG VAL ASP PRO VAL ASN PHE LYS LEU LEU SER HIS CYS SEQRES 9 A 141 LEU LEU VAL THR LEU ALA ALA HIS LEU PRO ALA GLU PHE SEQRES 10 A 141 THR PRO ALA VAL HIS ALA SER LEU ASP LYS PHE LEU ALA SEQRES 11 A 141 SER VAL SER THR VAL LEU THR SER LYS TYR ARG SEQRES 1 B 146 VAL HIS LEU THR PRO GLU GLU LYS SER ALA VAL THR ALA SEQRES 2 B 146 LEU TRP GLY LYS VAL ASN VAL ASP GLU VAL GLY GLY GLU SEQRES 3 B 146 ALA LEU GLY ARG LEU LEU VAL VAL TYR PRO TRP THR GLN SEQRES 4 B 146 ARG PHE PHE GLU SER PHE GLY ASP LEU SER THR PRO ASP SEQRES 5 B 146 ALA VAL MET GLY ASN PRO LYS VAL LYS ALA HIS GLY LYS SEQRES 6 B 146 LYS VAL LEU GLY ALA PHE SER ASP GLY LEU ALA HIS LEU SEQRES 7 B 146 ASP ASN LEU LYS GLY THR PHE ALA THR LEU SER GLU LEU SEQRES 8 B 146 HIS CYS ASP LYS LEU HIS VAL ASP PRO GLU ASN PHE ARG SEQRES 9 B 146 LEU LEU GLY ASN VAL LEU VAL CYS VAL LEU ALA HIS HIS SEQRES 10 B 146 PHE GLY LYS GLU PHE THR PRO PRO VAL GLN ALA ALA TYR SEQRES 11 B 146 GLN LYS VAL VAL ALA GLY VAL ALA ASN ALA LEU ALA HIS SEQRES 12 B 146 LYS TYR HIS HET HEM A 142 43 HET O2 A 143 2 HET MBN 1201 7 HET MBN 1202 7 HET HEM B 147 43 HET O2 B 148 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM O2 OXYGEN MOLECULE HETNAM MBN TOLUENE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 O2 2(O2) FORMUL 5 MBN 2(C7 H8) FORMUL 9 HOH *283(H2 O1) HELIX 1 1 SER A 3 GLY A 18 1 16 HELIX 2 2 HIS A 20 PHE A 36 1 17 HELIX 3 3 PRO A 37 PHE A 43 5 7 HELIX 4 4 SER A 52 HIS A 72 1 21 HELIX 5 5 ASP A 75 LEU A 80 1 6 HELIX 6 6 LEU A 80 LYS A 90 1 11 HELIX 7 7 ASP A 94 LEU A 113 1 20 HELIX 8 8 THR A 118 THR A 137 1 20 HELIX 9 9 THR B 4 GLY B 16 1 13 HELIX 10 10 GLU B 22 TYR B 35 1 14 HELIX 11 11 PRO B 36 GLY B 46 5 11 HELIX 12 12 THR B 50 ASN B 57 1 8 HELIX 13 13 ASN B 57 ALA B 76 1 20 HELIX 14 14 ASN B 80 PHE B 85 1 6 HELIX 15 15 PHE B 85 ASP B 94 1 10 HELIX 16 16 PRO B 100 GLY B 119 1 20 HELIX 17 17 LYS B 120 PHE B 122 5 3 HELIX 18 18 THR B 123 ALA B 142 1 20 HELIX 19 19 HIS B 143 HIS B 146 5 4 LINK FE HEM A 142 NE2 HIS A 87 LINK FE HEM A 142 O1 O2 A 143 LINK FE HEM B 147 NE2 HIS B 92 LINK FE HEM B 147 O1 O2 B 148 CRYST1 53.435 53.435 191.709 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 0.018714 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018714 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005216 0.00000