HEADER OXYGEN TRANSPORT 14-MAY-12 4F6D TITLE OXY STRUCTURE OF HIS100PHE CEREBRATULUS LACTEUS MINI-HEMOGLOBIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEURAL HEMOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NRHB; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CEREBRATULUS LACTEUS; SOURCE 3 ORGANISM_COMMON: MILKY RIBBON WORM; SOURCE 4 ORGANISM_TAXID: 6221; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXYGEN-STORAGE, APOLAR TUNNEL, OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.SOMAN,M.D.SALTER,J.S.OLSON REVDAT 2 28-FEB-24 4F6D 1 REMARK SEQADV LINK REVDAT 1 30-MAY-12 4F6D 0 JRNL AUTH J.SOMAN,M.D.SALTER,J.S.OLSON JRNL TITL OXY STRUCTURE OF HIS100PHE CEREBRATULUS LACTEUS JRNL TITL 2 MINI-HEMOGLOBIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 10018 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1004 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 27.0773 - 3.4420 0.93 1365 153 0.1719 0.1701 REMARK 3 2 3.4420 - 2.7328 0.95 1307 145 0.1687 0.1898 REMARK 3 3 2.7328 - 2.3876 0.94 1286 144 0.1661 0.2080 REMARK 3 4 2.3876 - 2.1694 0.94 1274 141 0.1633 0.2169 REMARK 3 5 2.1694 - 2.0140 0.94 1277 143 0.1727 0.1947 REMARK 3 6 2.0140 - 1.8953 0.93 1244 138 0.1632 0.2229 REMARK 3 7 1.8953 - 1.8004 0.93 1261 140 0.1729 0.2474 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 37.64 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.17050 REMARK 3 B22 (A**2) : -0.29520 REMARK 3 B33 (A**2) : 0.12470 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.025 894 REMARK 3 ANGLE : 0.922 1223 REMARK 3 CHIRALITY : 0.059 119 REMARK 3 PLANARITY : 0.003 157 REMARK 3 DIHEDRAL : 14.651 298 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 4F6D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072511. 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 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5412 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 : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10039 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.09800 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CRYSTALLIZED FROM 2.5 MM REMARK 280 AMMONIUM SULFATE AND 0.1M SODIUM CITRATE, PH 5.4, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 21.26400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.74900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.74250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.74900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.26400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.74250 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 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 16 NZ REMARK 480 LYS A 36 CD CE NZ 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 O HOH A 402 O HOH A 407 1.93 REMARK 500 O HOH A 460 O HOH A 462 2.02 REMARK 500 O HOH A 442 O HOH A 448 2.13 REMARK 500 ND1 HIS A 18 O HOH A 449 2.15 REMARK 500 O HOH A 386 O HOH A 405 2.19 REMARK 500 O HOH A 338 O HOH A 421 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 69 NE2 REMARK 620 2 HEM A 201 NA 90.9 REMARK 620 3 HEM A 201 NB 91.0 88.8 REMARK 620 4 HEM A 201 NC 86.1 176.4 89.2 REMARK 620 5 HEM A 201 ND 86.4 90.7 177.4 91.1 REMARK 620 6 OXY A 202 O1 176.0 92.5 91.0 90.6 91.6 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXY A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F68 RELATED DB: PDB REMARK 900 RELATED ID: 4F69 RELATED DB: PDB REMARK 900 RELATED ID: 4F6F RELATED DB: PDB REMARK 900 RELATED ID: 4F6G RELATED DB: PDB REMARK 900 RELATED ID: 4F6I RELATED DB: PDB REMARK 900 RELATED ID: 4F6J RELATED DB: PDB REMARK 900 RELATED ID: 4F6B RELATED DB: PDB DBREF 4F6D A 0 109 UNP O76242 GLBN_CERLA 1 110 SEQADV 4F6D PHE A 100 UNP O76242 HIS 101 ENGINEERED MUTATION SEQRES 1 A 110 MET VAL ASN TRP ALA ALA VAL VAL ASP ASP PHE TYR GLN SEQRES 2 A 110 GLU LEU PHE LYS ALA HIS PRO GLU TYR GLN ASN LYS PHE SEQRES 3 A 110 GLY PHE LYS GLY VAL ALA LEU GLY SER LEU LYS GLY ASN SEQRES 4 A 110 ALA ALA TYR LYS THR GLN ALA GLY LYS THR VAL ASP TYR SEQRES 5 A 110 ILE ASN ALA ALA ILE GLY GLY SER ALA ASP ALA ALA GLY SEQRES 6 A 110 LEU ALA SER ARG HIS LYS GLY ARG ASN VAL GLY SER ALA SEQRES 7 A 110 GLU PHE HIS ASN ALA LYS ALA CYS LEU ALA LYS ALA CYS SEQRES 8 A 110 SER ALA HIS GLY ALA PRO ASP LEU GLY PHE ALA ILE ASP SEQRES 9 A 110 ASP ILE LEU SER HIS LEU HET HEM A 201 43 HET OXY A 202 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM OXY OXYGEN MOLECULE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 OXY O2 FORMUL 4 HOH *164(H2 O) HELIX 1 1 ASN A 2 HIS A 18 1 17 HELIX 2 2 PRO A 19 PHE A 25 5 7 HELIX 3 3 ALA A 31 GLY A 37 5 7 HELIX 4 4 ASN A 38 GLY A 58 1 21 HELIX 5 5 ASP A 61 GLY A 71 1 11 HELIX 6 6 GLY A 75 ALA A 92 1 18 HELIX 7 7 LEU A 98 SER A 107 1 10 LINK NE2 HIS A 69 FE HEM A 201 1555 1555 2.13 LINK FE HEM A 201 O1 OXY A 202 1555 1555 1.86 SITE 1 AC1 20 MET A 0 LYS A 24 PHE A 25 GLN A 44 SITE 2 AC1 20 LYS A 47 TYR A 51 LEU A 65 ARG A 68 SITE 3 AC1 20 HIS A 69 ARG A 72 VAL A 74 PHE A 79 SITE 4 AC1 20 LEU A 86 ILE A 102 OXY A 202 HOH A 313 SITE 5 AC1 20 HOH A 317 HOH A 325 HOH A 356 HOH A 461 SITE 1 AC2 4 TYR A 11 PHE A 25 GLN A 44 HEM A 201 CRYST1 42.528 43.485 59.498 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 0.023514 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016807 0.00000