HEADER OXYGEN TRANSPORT 14-MAY-12 4F69 TITLE CARBONMONOXY STRUCTURE OF TYR11PHE/GLN44LEU/THR48VAL/ALA55TRP TITLE 2 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 4F69 1 REMARK SEQADV REVDAT 1 30-MAY-12 4F69 0 JRNL AUTH J.SOMAN,M.D.SALTER,J.S.OLSON JRNL TITL CARBONMONOXY STRUCTURE OF JRNL TITL 2 TYR11PHE/GLN44LEU/THR48VAL/ALA55TRP CEREBRATULUS LACTEUS JRNL TITL 3 MINI-HEMOGLOBIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 14636 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1464 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 27.0794 - 3.4455 0.96 1411 157 0.1984 0.2000 REMARK 3 2 3.4455 - 2.7357 1.00 1372 153 0.1788 0.2205 REMARK 3 3 2.7357 - 2.3901 0.99 1354 150 0.2004 0.1992 REMARK 3 4 2.3901 - 2.1717 0.99 1337 149 0.1862 0.2507 REMARK 3 5 2.1717 - 2.0161 0.98 1331 147 0.1898 0.2235 REMARK 3 6 2.0161 - 1.8972 0.98 1318 147 0.2013 0.2342 REMARK 3 7 1.8972 - 1.8022 0.97 1291 144 0.2340 0.3099 REMARK 3 8 1.8022 - 1.7238 0.96 1306 145 0.3093 0.3661 REMARK 3 9 1.7238 - 1.6575 0.96 1265 140 0.3746 0.4273 REMARK 3 10 1.6575 - 1.6003 0.90 1187 132 0.4817 0.4777 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.47 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 36.37 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.630 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.09600 REMARK 3 B22 (A**2) : -2.87250 REMARK 3 B33 (A**2) : -6.22350 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 : 0.008 899 REMARK 3 ANGLE : 0.973 1227 REMARK 3 CHIRALITY : 0.060 119 REMARK 3 PLANARITY : 0.004 155 REMARK 3 DIHEDRAL : 14.584 295 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 4F69 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_1000072507. 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 IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK 9.9.8.9 W9RSSI REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14641 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 27.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 2.620 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.14 REMARK 200 R MERGE FOR SHELL (I) : 0.31200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 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 21.32500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.75000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.68000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.75000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.32500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.68000 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 324 O HOH A 334 1.88 REMARK 500 C CMO A 201 FE HEM A 203 2.00 REMARK 500 O HOH A 317 O HOH A 351 2.06 REMARK 500 O HOH A 364 O HOH A 400 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 203 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 69 NE2 REMARK 620 2 HEM A 203 NA 87.4 REMARK 620 3 HEM A 203 NB 88.4 90.8 REMARK 620 4 HEM A 203 NC 89.4 176.7 88.5 REMARK 620 5 HEM A 203 ND 87.5 89.0 175.9 91.5 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 CMO A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F68 RELATED DB: PDB REMARK 900 RELATED ID: 4F6D 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 4F69 A 0 109 UNP O76242 GLBN_CERLA 1 110 SEQADV 4F69 PHE A 11 UNP O76242 TYR 12 ENGINEERED MUTATION SEQADV 4F69 LEU A 44 UNP O76242 GLN 45 ENGINEERED MUTATION SEQADV 4F69 VAL A 48 UNP O76242 THR 49 ENGINEERED MUTATION SEQADV 4F69 TRP A 55 UNP O76242 ALA 56 ENGINEERED MUTATION SEQRES 1 A 110 MET VAL ASN TRP ALA ALA VAL VAL ASP ASP PHE PHE 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 LEU ALA GLY LYS VAL VAL ASP TYR SEQRES 5 A 110 ILE ASN ALA TRP 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 HIS ALA ILE ASP SEQRES 9 A 110 ASP ILE LEU SER HIS LEU HET CMO A 201 2 HET GOL A 202 6 HET HEM A 203 43 HETNAM CMO CARBON MONOXIDE HETNAM GOL GLYCEROL HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN HEM HEME FORMUL 2 CMO C O FORMUL 3 GOL C3 H8 O3 FORMUL 4 HEM C34 H32 FE N4 O4 FORMUL 5 HOH *125(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 57 1 20 HELIX 5 5 ASP A 61 GLY A 71 1 11 HELIX 6 6 GLY A 75 HIS A 93 1 19 HELIX 7 7 LEU A 98 SER A 107 1 10 LINK NE2 HIS A 69 FE HEM A 203 1555 1555 2.11 SITE 1 AC1 4 PHE A 11 PHE A 25 LEU A 44 HEM A 203 SITE 1 AC2 3 ASN A 2 HIS A 93 HOH A 420 SITE 1 AC3 20 PHE A 10 LYS A 24 PHE A 25 LYS A 47 SITE 2 AC3 20 LEU A 65 ARG A 68 HIS A 69 ARG A 72 SITE 3 AC3 20 VAL A 74 GLU A 78 PHE A 79 ILE A 102 SITE 4 AC3 20 CMO A 201 HOH A 317 HOH A 322 HOH A 323 SITE 5 AC3 20 HOH A 351 HOH A 363 HOH A 398 HOH A 425 CRYST1 42.650 43.360 59.500 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 0.023447 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016807 0.00000