HEADER OXYGEN STORAGE/TRANSPORT 13-DEC-99 1DLW TITLE X-RAY CRYSTAL STRUCTURE OF TRUNCATED HEMOGLOBIN FROM P.CAUDATUM. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARAMECIUM CAUDATUM; SOURCE 3 ORGANISM_TAXID: 5885; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLOBIN FOLD TRUNCATED HEMOGLOBIN NON VERTEBRATE HEMOGLOBIN, OXYGEN KEYWDS 2 STORAGE-TRANSPORT COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.PESCE,M.COUTURE,M.GUERTIN,S.DEWILDE,L.MOENS,M.BOLOGNESI REVDAT 3 07-FEB-24 1DLW 1 REMARK LINK REVDAT 2 24-FEB-09 1DLW 1 VERSN REVDAT 1 20-SEP-00 1DLW 0 JRNL AUTH A.PESCE,M.COUTURE,S.DEWILDE,M.GUERTIN,K.YAMAUCHI,P.ASCENZI, JRNL AUTH 2 L.MOENS,M.BOLOGNESI JRNL TITL A NOVEL TWO-OVER-TWO ALPHA-HELICAL SANDWICH FOLD IS JRNL TITL 2 CHARACTERISTIC OF THE TRUNCATED HEMOGLOBIN FAMILY. JRNL REF EMBO J. V. 19 2424 2000 JRNL REFN ISSN 0261-4189 JRNL PMID 10835341 JRNL DOI 10.1093/EMBOJ/19.11.2424 REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 36762 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3672 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 837 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 207 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.570 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AT THE END OF REFINEMENT, THE REMARK 3 ANISOTROPIC REFINEMENT OF B-FACTORS WAS USED. REMARK 4 REMARK 4 1DLW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36762 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.02500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.10600 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: NULL REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, SODIUM ACETATE, PH REMARK 280 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 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 17.89500 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 26.84250 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 8.94750 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 400 REMARK 400 COMPOUND REMARK 400 TRUNCATED HEMOGLOBIN OF 116 AMINO ACID RESIDUES PER CHAIN 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 GLU A 107 O HOH A 158 0.25 REMARK 500 CB GLN A 9 O HOH A 146 0.31 REMARK 500 OD1 ASN A 57 O HOH A 201 0.32 REMARK 500 CD2 PHE A 3 O HOH A 212 0.45 REMARK 500 N THR A 108 O HOH A 168 0.51 REMARK 500 CE2 PHE A 3 O HOH A 212 0.95 REMARK 500 CG ASN A 57 O HOH A 201 1.01 REMARK 500 CD GLU A 107 O HOH A 158 1.05 REMARK 500 CB ASN A 70 O HOH A 271 1.17 REMARK 500 C GLU A 107 O HOH A 168 1.25 REMARK 500 CA GLN A 9 O HOH A 146 1.25 REMARK 500 CG PHE A 3 O HOH A 212 1.72 REMARK 500 CG GLN A 9 O HOH A 146 1.75 REMARK 500 OE2 GLU A 107 O HOH A 158 1.95 REMARK 500 CA THR A 108 O HOH A 168 1.97 REMARK 500 CA GLU A 107 O HOH A 168 2.05 REMARK 500 ND2 ASN A 57 O HOH A 201 2.08 REMARK 500 CZ PHE A 3 O HOH A 212 2.09 REMARK 500 CA ASN A 70 O HOH A 271 2.12 REMARK 500 N GLN A 9 O HOH A 146 2.13 REMARK 500 O HOH A 298 O HOH A 318 2.14 REMARK 500 CB ASN A 57 O HOH A 201 2.16 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 144 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 68 NE2 REMARK 620 2 HEM A 144 NA 92.3 REMARK 620 3 HEM A 144 NB 93.4 91.3 REMARK 620 4 HEM A 144 NC 96.8 170.9 88.4 REMARK 620 5 HEM A 144 ND 96.1 89.6 170.4 89.2 REMARK 620 6 HOH A 351 O 172.2 80.4 84.2 90.5 86.6 REMARK 620 N 1 2 3 4 5 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 144 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DLY RELATED DB: PDB REMARK 900 TRUNCATED HEMOGLOBIN, WITH 121 AMINO ACID RESIDUES PER CHAIN. DBREF 1DLW A 1 116 UNP P15160 GLB_PARCA 1 116 SEQRES 1 A 116 SER LEU PHE GLU GLN LEU GLY GLY GLN ALA ALA VAL GLN SEQRES 2 A 116 ALA VAL THR ALA GLN PHE TYR ALA ASN ILE GLN ALA ASP SEQRES 3 A 116 ALA THR VAL ALA THR PHE PHE ASN GLY ILE ASP MET PRO SEQRES 4 A 116 ASN GLN THR ASN LYS THR ALA ALA PHE LEU CYS ALA ALA SEQRES 5 A 116 LEU GLY GLY PRO ASN ALA TRP THR GLY ARG ASN LEU LYS SEQRES 6 A 116 GLU VAL HIS ALA ASN MET GLY VAL SER ASN ALA GLN PHE SEQRES 7 A 116 THR THR VAL ILE GLY HIS LEU ARG SER ALA LEU THR GLY SEQRES 8 A 116 ALA GLY VAL ALA ALA ALA LEU VAL GLU GLN THR VAL ALA SEQRES 9 A 116 VAL ALA GLU THR VAL ARG GLY ASP VAL VAL THR VAL HET HEM A 144 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *207(H2 O) HELIX 1 1 SER A 1 LEU A 6 1 6 HELIX 2 2 GLY A 8 ALA A 25 1 18 HELIX 3 3 VAL A 29 ASN A 34 5 6 HELIX 4 4 ASP A 37 LEU A 53 1 17 HELIX 5 5 ASN A 63 ALA A 69 1 7 HELIX 6 6 SER A 74 ALA A 92 1 19 HELIX 7 7 ALA A 95 THR A 108 1 14 HELIX 8 8 VAL A 109 VAL A 114 1 6 LINK NE2 HIS A 68 FE HEM A 144 1555 1555 2.14 LINK FE HEM A 144 O HOH A 351 1555 1555 2.09 SITE 1 AC1 17 PHE A 32 PHE A 33 ILE A 36 GLN A 41 SITE 2 AC1 17 TRP A 59 ARG A 62 LEU A 64 VAL A 67 SITE 3 AC1 17 HIS A 68 MET A 71 VAL A 73 VAL A 81 SITE 4 AC1 17 HOH A 205 HOH A 223 HOH A 248 HOH A 276 SITE 5 AC1 17 HOH A 351 CRYST1 61.180 61.180 35.790 90.00 90.00 90.00 P 43 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 0.016345 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016345 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027941 0.00000