HEADER OXYGEN TRANSPORT 14-MAY-12 4F6B TITLE AQUOMET 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 4F6B 1 REMARK SEQADV REVDAT 1 30-MAY-12 4F6B 0 JRNL AUTH J.SOMAN,M.D.SALTER,J.S.OLSON JRNL TITL AQUOMET STRUCTURE OF HIS100PHE CEREBRATULUS LACTEUS JRNL TITL 2 MINI-HEMOGLOBIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.64 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 13789 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1379 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 24.5481 - 3.5309 0.98 1341 146 0.1652 0.1886 REMARK 3 2 3.5309 - 2.8039 0.98 1278 143 0.1782 0.2074 REMARK 3 3 2.8039 - 2.4498 0.99 1241 138 0.1805 0.1905 REMARK 3 4 2.4498 - 2.2260 0.99 1254 140 0.1715 0.1823 REMARK 3 5 2.2260 - 2.0665 0.98 1232 137 0.1643 0.1858 REMARK 3 6 2.0665 - 1.9447 0.98 1226 136 0.1682 0.1879 REMARK 3 7 1.9447 - 1.8474 0.97 1203 134 0.1787 0.1952 REMARK 3 8 1.8474 - 1.7670 0.97 1232 137 0.2161 0.2610 REMARK 3 9 1.7670 - 1.6990 0.98 1195 133 0.2405 0.2863 REMARK 3 10 1.6990 - 1.6404 0.97 1208 135 0.3021 0.3107 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 34.96 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.84720 REMARK 3 B22 (A**2) : -3.07070 REMARK 3 B33 (A**2) : 3.91780 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 : 0.007 904 REMARK 3 ANGLE : 0.943 1235 REMARK 3 CHIRALITY : 0.069 119 REMARK 3 PLANARITY : 0.004 157 REMARK 3 DIHEDRAL : 14.800 300 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 30.6975 35.8164 10.5637 REMARK 3 T TENSOR REMARK 3 T11: 0.0684 T22: 0.0893 REMARK 3 T33: 0.0814 T12: -0.0034 REMARK 3 T13: 0.0005 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.4003 L22: 0.7054 REMARK 3 L33: 0.9945 L12: 0.2391 REMARK 3 L13: -0.6015 L23: -0.1412 REMARK 3 S TENSOR REMARK 3 S11: 0.0005 S12: -0.0459 S13: 0.0240 REMARK 3 S21: 0.0295 S22: 0.0180 S23: -0.0168 REMARK 3 S31: 0.0110 S32: 0.1309 S33: -0.0191 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 4F6B 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_1000072509. 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 REMARK 200 DATA SCALING SOFTWARE : D*TREK, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13828 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 49.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.11200 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 (%): 48.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 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 21.34000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.74000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.73500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.74000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.34000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.73500 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 437 O HOH A 438 1.91 REMARK 500 O HOH A 373 O HOH A 412 2.05 REMARK 500 O1 SO4 A 202 O HOH A 316 2.12 REMARK 500 O HOH A 391 O HOH A 417 2.15 REMARK 500 O HOH A 360 O HOH A 395 2.16 REMARK 500 O HOH A 383 O HOH A 418 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 365 O HOH A 387 2675 2.06 REMARK 500 O HOH A 365 O HOH A 407 2675 2.14 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 93.6 REMARK 620 3 HEM A 201 NB 92.4 89.7 REMARK 620 4 HEM A 201 NC 90.5 175.7 88.9 REMARK 620 5 HEM A 201 ND 90.7 90.4 176.8 90.8 REMARK 620 6 HOH A 301 O 177.3 87.1 85.0 88.7 91.8 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 SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 203 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: 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 4F6B A 0 109 UNP O76242 GLBN_CERLA 1 110 SEQADV 4F6B 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 SO4 A 202 10 HET GOL A 203 6 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN HEM HEME HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 SO4 O4 S 2- FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *148(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 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 2.11 LINK FE HEM A 201 O HOH A 301 1555 1555 2.25 SITE 1 AC1 20 MET A 0 PHE A 10 LYS A 24 PHE A 25 SITE 2 AC1 20 GLN A 44 LYS A 47 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 ILE A 102 SO4 A 202 HOH A 301 HOH A 320 SITE 5 AC1 20 HOH A 322 HOH A 326 HOH A 333 HOH A 386 SITE 1 AC2 12 MET A 0 VAL A 1 TRP A 3 ALA A 31 SITE 2 AC2 12 ARG A 68 HEM A 201 HOH A 307 HOH A 315 SITE 3 AC2 12 HOH A 316 HOH A 317 HOH A 378 HOH A 386 SITE 1 AC3 3 ASN A 2 HIS A 93 HOH A 404 CRYST1 42.680 43.470 59.480 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 0.023430 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016812 0.00000