HEADER OXYGEN TRANSPORT 16-SEP-09 2WTH TITLE LOW RESOLUTION 3D STRUCTURE OF C.ELEGANS GLOBIN-LIKE PROTEIN (GLB-1): TITLE 2 P3121 CRYSTAL FORM CAVEAT 2WTH ALA A 25 C-ALPHA IS PLANAR GLU B 24 C-ALPHA IS PLANAR COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLOBIN-LIKE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METAL-BINDING, OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR E.GEUENS,D.HOOGEWIJS,M.NARDINI,E.VINCK,A.PESCE,L.KIGER,A.FAGO, AUTHOR 2 L.TILLEMAN,S.DE HENAU,M.MARDEN,R.E.WEBER,S.VAN DOORSLAER, AUTHOR 3 J.VANFLETEREN,L.MOENS,M.BOLOGNESI,S.DEWILDE REVDAT 2 20-DEC-23 2WTH 1 REMARK LINK REVDAT 1 21-APR-10 2WTH 0 JRNL AUTH E.GEUENS,D.HOOGEWIJS,M.NARDINI,E.VINCK,A.PESCE,L.KIGER, JRNL AUTH 2 A.FAGO,L.TILLEMAN,S.DE HENAU,M.MARDEN,R.E.WEBER, JRNL AUTH 3 S.VAN DOORSLAER,J.VANFLETEREN,L.MOENS,M.BOLOGNESI,S.DEWILDE JRNL TITL GLOBIN-LIKE PROTEINS IN CAENORHABDITIS ELEGANS: IN VIVO JRNL TITL 2 LOCALIZATION, LIGAND BINDING AND STRUCTURAL PROPERTIES. JRNL REF BMC BIOCHEM. V. 11 17 2010 JRNL REFN ESSN 1471-2091 JRNL PMID 20361867 JRNL DOI 10.1186/1471-2091-11-17 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 12139 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.271 REMARK 3 R VALUE (WORKING SET) : 0.269 REMARK 3 FREE R VALUE : 0.319 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 627 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 867 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.3340 REMARK 3 BIN FREE R VALUE SET COUNT : 57 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2588 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 141 REMARK 3 SOLVENT ATOMS : 46 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.69000 REMARK 3 B22 (A**2) : 0.69000 REMARK 3 B33 (A**2) : -1.04000 REMARK 3 B12 (A**2) : 0.35000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.428 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.381 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 39.480 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.883 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.819 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2666 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3617 ; 0.996 ; 2.041 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 314 ; 4.649 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 135 ;37.808 ;24.074 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 384 ;17.442 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ; 9.200 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 344 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2101 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1377 ; 0.194 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1831 ; 0.296 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 96 ; 0.136 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 30 ; 0.162 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.123 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1578 ; 0.736 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2445 ; 1.339 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1244 ; 1.152 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1168 ; 1.593 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2WTH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1290041169. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12777 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 34.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2WTG REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.0 M AMMONIUM SULPHATE, 10% GLYCEROL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.54667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 97.09333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 97.09333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 48.54667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.4 KCAL/MOL 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 127 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN B, CYS 127 TO SER REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 MET B 1 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 14 CG CD CE NZ REMARK 480 THR A 23 CG2 REMARK 480 ALA A 25 CB REMARK 480 GLN A 26 CB CG CD OE1 NE2 REMARK 480 ILE A 28 CB CG1 CG2 CD1 REMARK 480 LYS A 50 CD CE NZ REMARK 480 ALA A 57 CB REMARK 480 LYS A 61 CG CD CE NZ REMARK 480 LYS A 62 CB CG CD CE NZ REMARK 480 LYS A 68 CB CG CD CE NZ REMARK 480 ARG A 100 NE CZ NH1 NH2 REMARK 480 ARG A 102 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 105 CE NZ REMARK 480 VAL A 125 CB CG1 CG2 REMARK 480 GLN A 131 CD OE1 NE2 REMARK 480 LYS A 133 CG CD CE NZ REMARK 480 LYS A 141 CG CD CE NZ REMARK 480 ALA A 145 CB REMARK 480 THR A 149 CG2 REMARK 480 LEU A 151 CG CD1 CD2 REMARK 480 LYS A 152 CB CG CD CE NZ REMARK 480 SER B 2 CB OG REMARK 480 GLU B 7 CB CG CD OE1 OE2 REMARK 480 LYS B 14 CB CG CD CE NZ REMARK 480 THR B 23 CG2 REMARK 480 GLU B 24 CB CG CD OE1 OE2 REMARK 480 ALA B 25 CB REMARK 480 ILE B 28 CG1 CG2 CD1 REMARK 480 LYS B 54 CD CE NZ REMARK 480 ALA B 57 CB REMARK 480 LYS B 61 CG CD CE NZ REMARK 480 LYS B 62 CG CD CE NZ REMARK 480 GLU B 64 CG CD OE1 OE2 REMARK 480 ARG B 102 NE CZ NH1 NH2 REMARK 480 VAL B 125 CG1 CG2 REMARK 480 SER B 127 CB OG REMARK 480 LYS B 152 CB CG CD CE NZ REMARK 480 ASN B 155 CB CG OD1 ND2 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 OD1 ASN B 4 OE1 GLU B 7 2.01 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 NZ LYS A 141 O3 GOL B 1162 4655 1.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LEU A 11 C CYS A 12 N 0.181 REMARK 500 ALA A 25 CA ALA A 25 CB -0.186 REMARK 500 GLN A 26 CA GLN A 26 CB -0.281 REMARK 500 ILE A 28 CA ILE A 28 CB -0.176 REMARK 500 ALA A 57 CA ALA A 57 CB -0.135 REMARK 500 LYS A 62 CA LYS A 62 CB 0.480 REMARK 500 ARG A 100 CD ARG A 100 NE 0.111 REMARK 500 ARG A 102 CB ARG A 102 CG -0.301 REMARK 500 LYS A 105 CD LYS A 105 CE 0.304 REMARK 500 VAL A 125 CA VAL A 125 CB -0.311 REMARK 500 GLN A 132 CD GLN A 132 NE2 0.171 REMARK 500 ALA A 145 CA ALA A 145 CB 0.127 REMARK 500 THR A 149 CB THR A 149 CG2 0.308 REMARK 500 LYS A 152 CA LYS A 152 CB -0.184 REMARK 500 GLU B 7 CA GLU B 7 CB -0.218 REMARK 500 THR B 23 CB THR B 23 CG2 0.266 REMARK 500 GLU B 24 CA GLU B 24 CB -0.465 REMARK 500 LYS B 54 CG LYS B 54 CD -0.281 REMARK 500 LYS B 62 CB LYS B 62 CG -0.218 REMARK 500 GLU B 64 CB GLU B 64 CG -0.219 REMARK 500 VAL B 125 CB VAL B 125 CG1 -0.276 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 THR A 23 OG1 - CB - CG2 ANGL. DEV. = -28.8 DEGREES REMARK 500 ALA A 25 N - CA - CB ANGL. DEV. = 16.9 DEGREES REMARK 500 ALA A 57 N - CA - CB ANGL. DEV. = 9.2 DEGREES REMARK 500 LYS A 62 CB - CA - C ANGL. DEV. = -23.9 DEGREES REMARK 500 VAL A 125 CA - CB - CG2 ANGL. DEV. = -11.3 DEGREES REMARK 500 THR A 149 OG1 - CB - CG2 ANGL. DEV. = -23.8 DEGREES REMARK 500 THR A 149 CA - CB - CG2 ANGL. DEV. = -14.8 DEGREES REMARK 500 LEU A 151 CB - CG - CD2 ANGL. DEV. = 11.7 DEGREES REMARK 500 LYS A 152 N - CA - CB ANGL. DEV. = 24.2 DEGREES REMARK 500 LYS A 152 CA - CB - CG ANGL. DEV. = 18.6 DEGREES REMARK 500 GLU B 7 N - CA - CB ANGL. DEV. = 12.5 DEGREES REMARK 500 GLU B 24 CB - CA - C ANGL. DEV. = 13.8 DEGREES REMARK 500 GLU B 24 N - CA - CB ANGL. DEV. = 11.6 DEGREES REMARK 500 ALA B 25 N - CA - CB ANGL. DEV. = 14.0 DEGREES REMARK 500 ALA B 57 CB - CA - C ANGL. DEV. = 10.7 DEGREES REMARK 500 LYS B 62 CA - CB - CG ANGL. DEV. = 15.9 DEGREES REMARK 500 VAL B 125 CG1 - CB - CG2 ANGL. DEV. = 27.5 DEGREES REMARK 500 SER B 127 CB - CA - C ANGL. DEV. = -12.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 9 -72.43 -42.06 REMARK 500 GLU A 53 -6.74 -47.73 REMARK 500 LYS A 54 18.04 -141.46 REMARK 500 ARG A 100 2.44 -69.31 REMARK 500 LYS A 105 72.13 41.22 REMARK 500 PRO A 108 37.55 -70.46 REMARK 500 LYS B 105 76.79 24.85 REMARK 500 LYS B 152 -70.93 -53.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 102 0.09 SIDE CHAIN 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 160 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 101 NE2 REMARK 620 2 HEM A 160 NA 95.5 REMARK 620 3 HEM A 160 NB 94.0 87.7 REMARK 620 4 HEM A 160 NC 89.4 174.2 89.0 REMARK 620 5 HEM A 160 ND 89.9 89.6 175.5 93.5 REMARK 620 6 OXY A 161 O2 178.6 83.4 86.9 91.7 89.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 160 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 101 NE2 REMARK 620 2 HEM B 160 NA 94.9 REMARK 620 3 HEM B 160 NB 94.8 91.2 REMARK 620 4 HEM B 160 NC 94.0 170.9 86.1 REMARK 620 5 HEM B 160 ND 90.4 89.2 174.8 92.7 REMARK 620 6 OXY B 161 O2 175.1 81.2 88.3 90.1 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 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXY A 161 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXY B 161 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1164 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1161 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1162 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1165 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1161 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1162 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WTG RELATED DB: PDB REMARK 900 HIGH RESOLUTION 3D STRUCTURE OF C.ELEGANS GLOBIN-LIKE PROTEIN GLB-1 REMARK 999 REMARK 999 SEQUENCE REMARK 999 WITH RESPECT TO SEQUENCE PRESENT IN THE UNIPROT DATABASE, REMARK 999 CYS127 WAS MUTATED INTO SER RESIDUE FOR CRYSTALLIZATION REMARK 999 PURPOSE DBREF 2WTH A 1 159 UNP P30627 GLBH_CAEEL 1 159 DBREF 2WTH B 1 159 UNP P30627 GLBH_CAEEL 1 159 SEQADV 2WTH SER A 127 UNP P30627 CYS 127 ENGINEERED MUTATION SEQADV 2WTH SER B 127 UNP P30627 CYS 127 ENGINEERED MUTATION SEQRES 1 A 159 MET SER MET ASN ARG GLN GLU ILE SER ASP LEU CYS VAL SEQRES 2 A 159 LYS SER LEU GLU GLY ARG MET VAL GLY THR GLU ALA GLN SEQRES 3 A 159 ASN ILE GLU ASN GLY ASN ALA PHE TYR ARG TYR PHE PHE SEQRES 4 A 159 THR ASN PHE PRO ASP LEU ARG VAL TYR PHE LYS GLY ALA SEQRES 5 A 159 GLU LYS TYR THR ALA ASP ASP VAL LYS LYS SER GLU ARG SEQRES 6 A 159 PHE ASP LYS GLN GLY GLN ARG ILE LEU LEU ALA CYS HIS SEQRES 7 A 159 LEU LEU ALA ASN VAL TYR THR ASN GLU GLU VAL PHE LYS SEQRES 8 A 159 GLY TYR VAL ARG GLU THR ILE ASN ARG HIS ARG ILE TYR SEQRES 9 A 159 LYS MET ASP PRO ALA LEU TRP MET ALA PHE PHE THR VAL SEQRES 10 A 159 PHE THR GLY TYR LEU GLU SER VAL GLY SER LEU ASN ASP SEQRES 11 A 159 GLN GLN LYS ALA ALA TRP MET ALA LEU GLY LYS GLU PHE SEQRES 12 A 159 ASN ALA GLU SER GLN THR HIS LEU LYS ASN SER ASN LEU SEQRES 13 A 159 PRO HIS VAL SEQRES 1 B 159 MET SER MET ASN ARG GLN GLU ILE SER ASP LEU CYS VAL SEQRES 2 B 159 LYS SER LEU GLU GLY ARG MET VAL GLY THR GLU ALA GLN SEQRES 3 B 159 ASN ILE GLU ASN GLY ASN ALA PHE TYR ARG TYR PHE PHE SEQRES 4 B 159 THR ASN PHE PRO ASP LEU ARG VAL TYR PHE LYS GLY ALA SEQRES 5 B 159 GLU LYS TYR THR ALA ASP ASP VAL LYS LYS SER GLU ARG SEQRES 6 B 159 PHE ASP LYS GLN GLY GLN ARG ILE LEU LEU ALA CYS HIS SEQRES 7 B 159 LEU LEU ALA ASN VAL TYR THR ASN GLU GLU VAL PHE LYS SEQRES 8 B 159 GLY TYR VAL ARG GLU THR ILE ASN ARG HIS ARG ILE TYR SEQRES 9 B 159 LYS MET ASP PRO ALA LEU TRP MET ALA PHE PHE THR VAL SEQRES 10 B 159 PHE THR GLY TYR LEU GLU SER VAL GLY SER LEU ASN ASP SEQRES 11 B 159 GLN GLN LYS ALA ALA TRP MET ALA LEU GLY LYS GLU PHE SEQRES 12 B 159 ASN ALA GLU SER GLN THR HIS LEU LYS ASN SER ASN LEU SEQRES 13 B 159 PRO HIS VAL HET HEM A 160 43 HET OXY A 161 2 HET SO4 A1160 5 HET GOL A1161 6 HET GOL A1162 6 HET HEM B 160 43 HET OXY B 161 2 HET SO4 B1160 5 HET GOL B1161 6 HET GOL B1162 6 HET SO4 B1163 5 HET GOL B1164 6 HET GOL B1165 6 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM OXY OXYGEN MOLECULE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN HEM HEME HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 OXY 2(O2) FORMUL 5 SO4 3(O4 S 2-) FORMUL 6 GOL 6(C3 H8 O3) FORMUL 16 HOH *46(H2 O) HELIX 1 1 ASN A 4 GLU A 17 1 14 HELIX 2 2 GLU A 24 ASN A 30 1 7 HELIX 3 3 ASN A 32 PHE A 42 1 11 HELIX 4 4 PRO A 43 PHE A 49 5 7 HELIX 5 5 THR A 56 LYS A 62 1 7 HELIX 6 6 GLU A 64 GLN A 69 1 6 HELIX 7 7 GLN A 71 TYR A 84 1 14 HELIX 8 8 ASN A 86 LYS A 91 1 6 HELIX 9 9 TYR A 93 ARG A 100 1 8 HELIX 10 10 ALA A 109 THR A 119 1 11 HELIX 11 11 ASN A 129 LEU A 139 1 11 HELIX 12 12 LYS A 141 SER A 154 1 14 HELIX 13 13 ASN B 4 SER B 15 1 12 HELIX 14 14 GLU B 24 ASN B 30 1 7 HELIX 15 15 ASN B 32 PHE B 42 1 11 HELIX 16 16 PRO B 43 PHE B 49 5 7 HELIX 17 17 THR B 56 SER B 63 1 8 HELIX 18 18 GLU B 64 GLN B 69 1 6 HELIX 19 19 GLN B 71 TYR B 84 1 14 HELIX 20 20 ASN B 86 LYS B 91 1 6 HELIX 21 21 TYR B 93 ARG B 100 1 8 HELIX 22 22 ALA B 109 THR B 119 1 11 HELIX 23 23 ASN B 129 LEU B 139 1 11 HELIX 24 24 LYS B 141 ASN B 153 1 13 LINK NE2 HIS A 101 FE HEM A 160 1555 1555 2.17 LINK FE HEM A 160 O2 OXY A 161 1555 1555 2.37 LINK NE2 HIS B 101 FE HEM B 160 1555 1555 2.05 LINK FE HEM B 160 O2 OXY B 161 1555 1555 2.26 SITE 1 AC1 14 TYR A 48 PHE A 49 ARG A 65 GLN A 69 SITE 2 AC1 14 ARG A 72 ILE A 73 ALA A 76 THR A 97 SITE 3 AC1 14 ARG A 100 HIS A 101 TYR A 104 MET A 106 SITE 4 AC1 14 PHE A 114 OXY A 161 SITE 1 AC2 3 TYR A 35 ILE A 73 HEM A 160 SITE 1 AC3 14 TYR B 48 ARG B 65 GLN B 69 ILE B 73 SITE 2 AC3 14 ALA B 76 LEU B 80 THR B 97 ARG B 100 SITE 3 AC3 14 HIS B 101 TYR B 104 MET B 106 TRP B 111 SITE 4 AC3 14 PHE B 114 OXY B 161 SITE 1 AC4 2 ILE B 73 HEM B 160 SITE 1 AC5 3 SER B 63 GLU B 64 ARG B 65 SITE 1 AC6 7 ARG A 72 LEU A 75 LEU A 79 TYR A 93 SITE 2 AC6 7 TYR B 93 GLU B 96 ARG B 100 SITE 1 AC7 1 HOH B2024 SITE 1 AC8 3 ASN B 4 ARG B 5 GLN B 6 SITE 1 AC9 1 LYS B 105 SITE 1 BC1 1 HOH B2025 SITE 1 BC2 5 ASN A 4 ARG A 5 SER A 63 ARG A 65 SITE 2 BC2 5 GOL A1162 SITE 1 BC3 4 ARG A 5 TYR A 55 GOL A1161 HOH A2021 CRYST1 77.681 77.681 145.640 90.00 90.00 120.00 P 31 2 1 12 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 0.012873 0.007432 0.000000 0.00000 SCALE2 0.000000 0.014865 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006866 0.00000