HEADER TRANSFERASE 18-SEP-13 4MSO TITLE X-RAY CRYSTAL STRUCTURE OF A SERINE HYDROXYMETHYL TRANSFERASE IN APO TITLE 2 FORM FROM BURKHOLDERIA CENOCEPACIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROXYMETHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SHMT, SERINE METHYLASE; COMPND 5 EC: 2.1.2.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA CENOCEPACIA; SOURCE 3 ORGANISM_TAXID: 216591; SOURCE 4 STRAIN: J2315; SOURCE 5 GENE: GLYA, GLYA1, BCEJ2315_31420, BCAL3197; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURAL GENOMICS, NIAID, NATIONAL INSTITUTE OF ALLERGY AND KEYWDS 2 INFECTIOUS DISEASES, SEATTLE STRUCTURAL GENOMICS CENTER FOR KEYWDS 3 INFECTIOUS DISEASE, SSGCID, SERINE HYDROXYMETHYL TRANSFERASE, KEYWDS 4 TRANSFERASE, PYRIDOXAL PHOSPHATE EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 2 20-SEP-23 4MSO 1 REMARK SEQADV REVDAT 1 11-DEC-13 4MSO 0 JRNL AUTH J.W.FAIRMAN,M.M.JENSEN,A.H.SULLIVAN,J.ABENDROTH,T.E.EDWARDS, JRNL AUTH 2 D.LORIMER JRNL TITL X-RAY CRYSTAL STRUCTURE OF A SERINE HYDROXYMETHYL JRNL TITL 2 TRANSFERASE IN APO FORM FROM BURKHOLDERIA CENOCEPACIA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 144410 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) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7245 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 10054 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 REMARK 3 BIN FREE R VALUE SET COUNT : 502 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5698 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 754 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : -0.15000 REMARK 3 B33 (A**2) : 0.10000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.061 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.058 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.036 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.817 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6185 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6024 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8446 ; 1.698 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13842 ; 0.826 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 843 ; 7.389 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 261 ;35.039 ;24.636 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1014 ;11.569 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;14.354 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 973 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7178 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1361 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 3211 ; 1.956 ; 1.587 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3210 ; 1.963 ; 2.097 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4019 ; 2.409 ; 2.380 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 6170 ; 3.343 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6030 ;14.545 ; 5.000 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4MSO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082316. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 144410 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.55200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1DFO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MCSG1 G8: 0.2 M AMMONIUM SULFATE, 0.1 REMARK 280 M TRIS PH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K 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 27.64000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 91.06000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.29000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 91.06000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.64000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.29000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 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 -7 REMARK 465 ALA A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 57 REMARK 465 GLU A 58 REMARK 465 GLY A 59 REMARK 465 TYR A 60 REMARK 465 PRO A 61 REMARK 465 GLY A 62 REMARK 465 LYS A 63 REMARK 465 ARG A 64 REMARK 465 TYR A 65 REMARK 465 TYR A 66 REMARK 465 GLY A 67 REMARK 465 GLY A 68 REMARK 465 CYS A 69 REMARK 465 GLU A 70 REMARK 465 ALA A 123 REMARK 465 HIS A 124 REMARK 465 GLY A 125 REMARK 465 GLY A 126 REMARK 465 HIS A 127 REMARK 465 LEU A 128 REMARK 465 THR A 129 REMARK 465 HIS A 130 REMARK 465 ASN A 149 REMARK 465 GLU A 150 REMARK 465 ASN A 151 REMARK 465 GLU A 152 REMARK 465 ASP A 153 REMARK 465 SER A 309 REMARK 465 GLY A 310 REMARK 465 ARG A 311 REMARK 465 THR A 312 REMARK 465 MET B -7 REMARK 465 ALA B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ALA B 57 REMARK 465 GLU B 58 REMARK 465 GLY B 59 REMARK 465 TYR B 60 REMARK 465 PRO B 61 REMARK 465 GLY B 62 REMARK 465 LYS B 63 REMARK 465 ARG B 64 REMARK 465 TYR B 65 REMARK 465 TYR B 66 REMARK 465 GLY B 67 REMARK 465 GLY B 68 REMARK 465 CYS B 69 REMARK 465 GLU B 70 REMARK 465 ALA B 123 REMARK 465 HIS B 124 REMARK 465 GLY B 125 REMARK 465 GLY B 126 REMARK 465 HIS B 127 REMARK 465 LEU B 128 REMARK 465 THR B 129 REMARK 465 HIS B 130 REMARK 465 GLY B 131 REMARK 465 SER B 132 REMARK 465 PRO B 133 REMARK 465 VAL B 134 REMARK 465 ASN B 135 REMARK 465 MET B 136 REMARK 465 ASN B 149 REMARK 465 GLU B 150 REMARK 465 ASN B 151 REMARK 465 GLU B 152 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PHE A 2 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 4 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 56 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR A 71 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 161 CG CD CE NZ REMARK 470 LYS A 167 CG CD CE NZ REMARK 470 LYS A 181 CG CD CE NZ REMARK 470 LYS A 189 CG CD CE NZ REMARK 470 LYS A 302 CG CD CE NZ REMARK 470 GLU A 313 CG CD OE1 OE2 REMARK 470 PHE A 355 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 390 CG OD1 ND2 REMARK 470 PHE B 2 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 4 CG CD NE CZ NH1 NH2 REMARK 470 TYR B 56 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR B 71 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU B 122 CG CD1 CD2 REMARK 470 SER B 137 OG REMARK 470 ASP B 153 CG OD1 OD2 REMARK 470 LYS B 167 CG CD CE NZ REMARK 470 LYS B 169 CG CD CE NZ REMARK 470 LYS B 181 CG CD CE NZ REMARK 470 LYS B 248 CG CD CE NZ REMARK 470 ARG B 311 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 313 CG CD OE1 OE2 REMARK 470 LYS B 353 CG CD CE NZ REMARK 470 PHE B 355 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 398 CG CD OE1 OE2 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 NE2 GLN B 259 O HOH B 659 1.71 REMARK 500 O HOH A 865 O HOH A 877 1.72 REMARK 500 O LYS B 248 N SER B 252 1.98 REMARK 500 O ILE A 258 O HOH A 879 2.05 REMARK 500 O HOH A 865 O HOH A 887 2.09 REMARK 500 O HOH B 635 O HOH B 682 2.17 REMARK 500 O HOH B 778 O HOH B 832 2.18 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 B 192 O HOH A 968 4475 1.81 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 PHE A 255 CB - CA - C ANGL. DEV. = -12.1 DEGREES REMARK 500 PHE A 255 N - CA - C ANGL. DEV. = 19.6 DEGREES REMARK 500 PRO A 256 C - N - CA ANGL. DEV. = 53.9 DEGREES REMARK 500 PRO A 256 C - N - CD ANGL. DEV. = -57.7 DEGREES REMARK 500 PRO A 256 N - CA - C ANGL. DEV. = -15.7 DEGREES REMARK 500 PRO B 262 C - N - CA ANGL. DEV. = 9.3 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 LYS A 230 -137.72 74.04 REMARK 500 PRO A 256 -7.07 154.20 REMARK 500 HIS A 339 30.11 70.65 REMARK 500 HIS A 339 30.67 70.35 REMARK 500 VAL A 356 -62.79 -107.76 REMARK 500 THR A 357 163.31 69.32 REMARK 500 ASN A 390 65.22 -153.02 REMARK 500 PHE A 411 73.45 -119.86 REMARK 500 LYS B 230 -137.93 73.12 REMARK 500 PHE B 255 164.98 178.70 REMARK 500 PRO B 256 42.51 -103.42 REMARK 500 HIS B 339 31.44 70.17 REMARK 500 VAL B 356 -64.59 -108.17 REMARK 500 THR B 357 166.73 65.24 REMARK 500 ASN B 390 59.34 -147.67 REMARK 500 PHE B 411 72.85 -118.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE A 255 PRO A 256 147.78 REMARK 500 PHE B 255 PRO B 256 -132.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SSGCID-BUCEA.00008.A RELATED DB: TARGETTRACK DBREF 4MSO A 1 415 UNP B4ECY9 B4ECY9_BURCJ 1 415 DBREF 4MSO B 1 415 UNP B4ECY9 B4ECY9_BURCJ 1 415 SEQADV 4MSO MET A -7 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO ALA A -6 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO HIS A -5 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO HIS A -4 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO HIS A -3 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO HIS A -2 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO HIS A -1 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO HIS A 0 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO MET B -7 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO ALA B -6 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO HIS B -5 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO HIS B -4 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO HIS B -3 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO HIS B -2 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO HIS B -1 UNP B4ECY9 EXPRESSION TAG SEQADV 4MSO HIS B 0 UNP B4ECY9 EXPRESSION TAG SEQRES 1 A 423 MET ALA HIS HIS HIS HIS HIS HIS MET PHE ASP ARG ALA SEQRES 2 A 423 GLN SER THR ILE ALA ASN VAL ASP PRO GLU ILE PHE ALA SEQRES 3 A 423 ALA ILE GLU GLN GLU ASN ARG ARG GLN GLU ASP HIS ILE SEQRES 4 A 423 GLU LEU ILE ALA SER GLU ASN TYR THR SER PRO ALA VAL SEQRES 5 A 423 MET ALA ALA GLN GLY SER GLN LEU THR ASN LYS TYR ALA SEQRES 6 A 423 GLU GLY TYR PRO GLY LYS ARG TYR TYR GLY GLY CYS GLU SEQRES 7 A 423 TYR VAL ASP VAL VAL GLU GLN LEU ALA ILE ASP ARG VAL SEQRES 8 A 423 LYS GLN LEU PHE GLY ALA GLU ALA ALA ASN VAL GLN PRO SEQRES 9 A 423 ASN SER GLY SER GLN ALA ASN GLN GLY VAL PHE PHE ALA SEQRES 10 A 423 MET LEU LYS PRO GLY ASP THR ILE MET GLY MET SER LEU SEQRES 11 A 423 ALA HIS GLY GLY HIS LEU THR HIS GLY SER PRO VAL ASN SEQRES 12 A 423 MET SER GLY LYS TRP PHE ASN VAL VAL SER TYR GLY LEU SEQRES 13 A 423 ASN GLU ASN GLU ASP ILE ASP TYR ASP ALA ALA GLU LYS SEQRES 14 A 423 LEU ALA ASN GLU HIS LYS PRO LYS LEU ILE VAL ALA GLY SEQRES 15 A 423 ALA SER ALA PHE ALA LEU LYS ILE ASP PHE GLU ARG LEU SEQRES 16 A 423 ALA LYS ILE ALA LYS SER VAL GLY ALA TYR LEU MET VAL SEQRES 17 A 423 ASP MET ALA HIS TYR ALA GLY LEU ILE ALA ALA GLY VAL SEQRES 18 A 423 TYR PRO ASN PRO VAL PRO HIS ALA ASP PHE VAL THR THR SEQRES 19 A 423 THR THR HIS LYS SER LEU ARG GLY PRO ARG GLY GLY VAL SEQRES 20 A 423 ILE LEU MET LYS ALA GLU TYR GLU LYS PRO ILE ASN SER SEQRES 21 A 423 ALA ILE PHE PRO GLY ILE GLN GLY GLY PRO LEU MET HIS SEQRES 22 A 423 VAL ILE ALA ALA LYS ALA VAL ALA PHE LYS GLU ALA LEU SEQRES 23 A 423 SER PRO GLU PHE LYS GLU TYR GLN GLN LYS VAL VAL GLU SEQRES 24 A 423 ASN ALA ARG VAL LEU ALA GLU THR LEU VAL LYS ARG GLY SEQRES 25 A 423 LEU ARG ILE VAL SER GLY ARG THR GLU SER HIS VAL MET SEQRES 26 A 423 LEU VAL ASP LEU ARG ALA LYS HIS ILE THR GLY LYS ALA SEQRES 27 A 423 ALA GLU ALA ALA LEU GLY ALA ALA HIS ILE THR VAL ASN SEQRES 28 A 423 LYS ASN ALA ILE PRO ASN ASP PRO GLU LYS PRO PHE VAL SEQRES 29 A 423 THR SER GLY ILE ARG LEU GLY SER PRO ALA MET THR THR SEQRES 30 A 423 ARG GLY PHE GLY PRO ALA GLU ALA GLU GLN VAL GLY ASN SEQRES 31 A 423 LEU ILE ALA ASP VAL LEU GLU ASN PRO GLU ASP ALA ALA SEQRES 32 A 423 THR ILE GLU ARG VAL ARG ALA GLN VAL ALA GLU LEU THR SEQRES 33 A 423 LYS ARG PHE PRO VAL TYR ARG SEQRES 1 B 423 MET ALA HIS HIS HIS HIS HIS HIS MET PHE ASP ARG ALA SEQRES 2 B 423 GLN SER THR ILE ALA ASN VAL ASP PRO GLU ILE PHE ALA SEQRES 3 B 423 ALA ILE GLU GLN GLU ASN ARG ARG GLN GLU ASP HIS ILE SEQRES 4 B 423 GLU LEU ILE ALA SER GLU ASN TYR THR SER PRO ALA VAL SEQRES 5 B 423 MET ALA ALA GLN GLY SER GLN LEU THR ASN LYS TYR ALA SEQRES 6 B 423 GLU GLY TYR PRO GLY LYS ARG TYR TYR GLY GLY CYS GLU SEQRES 7 B 423 TYR VAL ASP VAL VAL GLU GLN LEU ALA ILE ASP ARG VAL SEQRES 8 B 423 LYS GLN LEU PHE GLY ALA GLU ALA ALA ASN VAL GLN PRO SEQRES 9 B 423 ASN SER GLY SER GLN ALA ASN GLN GLY VAL PHE PHE ALA SEQRES 10 B 423 MET LEU LYS PRO GLY ASP THR ILE MET GLY MET SER LEU SEQRES 11 B 423 ALA HIS GLY GLY HIS LEU THR HIS GLY SER PRO VAL ASN SEQRES 12 B 423 MET SER GLY LYS TRP PHE ASN VAL VAL SER TYR GLY LEU SEQRES 13 B 423 ASN GLU ASN GLU ASP ILE ASP TYR ASP ALA ALA GLU LYS SEQRES 14 B 423 LEU ALA ASN GLU HIS LYS PRO LYS LEU ILE VAL ALA GLY SEQRES 15 B 423 ALA SER ALA PHE ALA LEU LYS ILE ASP PHE GLU ARG LEU SEQRES 16 B 423 ALA LYS ILE ALA LYS SER VAL GLY ALA TYR LEU MET VAL SEQRES 17 B 423 ASP MET ALA HIS TYR ALA GLY LEU ILE ALA ALA GLY VAL SEQRES 18 B 423 TYR PRO ASN PRO VAL PRO HIS ALA ASP PHE VAL THR THR SEQRES 19 B 423 THR THR HIS LYS SER LEU ARG GLY PRO ARG GLY GLY VAL SEQRES 20 B 423 ILE LEU MET LYS ALA GLU TYR GLU LYS PRO ILE ASN SER SEQRES 21 B 423 ALA ILE PHE PRO GLY ILE GLN GLY GLY PRO LEU MET HIS SEQRES 22 B 423 VAL ILE ALA ALA LYS ALA VAL ALA PHE LYS GLU ALA LEU SEQRES 23 B 423 SER PRO GLU PHE LYS GLU TYR GLN GLN LYS VAL VAL GLU SEQRES 24 B 423 ASN ALA ARG VAL LEU ALA GLU THR LEU VAL LYS ARG GLY SEQRES 25 B 423 LEU ARG ILE VAL SER GLY ARG THR GLU SER HIS VAL MET SEQRES 26 B 423 LEU VAL ASP LEU ARG ALA LYS HIS ILE THR GLY LYS ALA SEQRES 27 B 423 ALA GLU ALA ALA LEU GLY ALA ALA HIS ILE THR VAL ASN SEQRES 28 B 423 LYS ASN ALA ILE PRO ASN ASP PRO GLU LYS PRO PHE VAL SEQRES 29 B 423 THR SER GLY ILE ARG LEU GLY SER PRO ALA MET THR THR SEQRES 30 B 423 ARG GLY PHE GLY PRO ALA GLU ALA GLU GLN VAL GLY ASN SEQRES 31 B 423 LEU ILE ALA ASP VAL LEU GLU ASN PRO GLU ASP ALA ALA SEQRES 32 B 423 THR ILE GLU ARG VAL ARG ALA GLN VAL ALA GLU LEU THR SEQRES 33 B 423 LYS ARG PHE PRO VAL TYR ARG HET PO4 A 501 5 HET PO4 A 502 5 HET EDO B 501 4 HET PO4 B 502 5 HETNAM PO4 PHOSPHATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 PO4 3(O4 P 3-) FORMUL 5 EDO C2 H6 O2 FORMUL 7 HOH *754(H2 O) HELIX 1 1 PHE A 2 ASN A 11 1 10 HELIX 2 2 ASP A 13 HIS A 30 1 18 HELIX 3 3 SER A 41 GLY A 49 1 9 HELIX 4 4 SER A 50 LYS A 55 5 6 HELIX 5 5 ASP A 73 GLY A 88 1 16 HELIX 6 6 SER A 98 LEU A 111 1 14 HELIX 7 7 ASP A 155 LYS A 167 1 13 HELIX 8 8 GLY A 174 LEU A 180 1 7 HELIX 9 9 ASP A 183 VAL A 194 1 12 HELIX 10 10 TYR A 205 ALA A 211 1 7 HELIX 11 11 HIS A 229 ARG A 233 5 5 HELIX 12 12 TYR A 246 ILE A 254 1 9 HELIX 13 13 PHE A 255 GLY A 260 1 6 HELIX 14 14 LEU A 263 LEU A 278 1 16 HELIX 15 15 SER A 279 ARG A 303 1 25 HELIX 16 16 ARG A 322 HIS A 325 5 4 HELIX 17 17 THR A 327 ALA A 338 1 12 HELIX 18 18 SER A 364 ARG A 370 1 7 HELIX 19 19 GLY A 373 ASN A 390 1 18 HELIX 20 20 ASP A 393 PHE A 411 1 19 HELIX 21 21 ASP B 3 SER B 7 1 5 HELIX 22 22 THR B 8 ALA B 10 5 3 HELIX 23 23 ASP B 13 HIS B 30 1 18 HELIX 24 24 SER B 41 GLY B 49 1 9 HELIX 25 25 SER B 50 LYS B 55 5 6 HELIX 26 26 ASP B 73 GLY B 88 1 16 HELIX 27 27 SER B 98 LEU B 111 1 14 HELIX 28 28 ASP B 155 LYS B 167 1 13 HELIX 29 29 GLY B 174 LEU B 180 1 7 HELIX 30 30 ASP B 183 VAL B 194 1 12 HELIX 31 31 TYR B 205 ALA B 211 1 7 HELIX 32 32 HIS B 229 ARG B 233 5 5 HELIX 33 33 TYR B 246 ALA B 253 1 8 HELIX 34 34 LEU B 263 SER B 279 1 17 HELIX 35 35 SER B 279 ARG B 303 1 25 HELIX 36 36 ARG B 322 HIS B 325 5 4 HELIX 37 37 THR B 327 ALA B 338 1 12 HELIX 38 38 SER B 364 ARG B 370 1 7 HELIX 39 39 GLY B 373 ASN B 390 1 18 HELIX 40 40 ASP B 393 PHE B 411 1 19 SHEET 1 A 2 ILE A 31 GLU A 32 0 SHEET 2 A 2 ILE A 340 THR A 341 1 O THR A 341 N ILE A 31 SHEET 1 B 7 ALA A 91 ASN A 93 0 SHEET 2 B 7 GLY A 238 MET A 242 -1 O ILE A 240 N ASN A 93 SHEET 3 B 7 PHE A 223 THR A 227 -1 N VAL A 224 O LEU A 241 SHEET 4 B 7 TYR A 197 ASP A 201 1 N VAL A 200 O THR A 225 SHEET 5 B 7 LEU A 170 ALA A 173 1 N ILE A 171 O TYR A 197 SHEET 6 B 7 THR A 116 SER A 121 1 N MET A 118 O VAL A 172 SHEET 7 B 7 ASN A 142 GLY A 147 1 O TYR A 146 N GLY A 119 SHEET 1 C 4 ARG A 306 ILE A 307 0 SHEET 2 C 4 VAL A 316 ASP A 320 -1 O ASP A 320 N ARG A 306 SHEET 3 C 4 GLY A 359 GLY A 363 -1 O ILE A 360 N VAL A 319 SHEET 4 C 4 ASN A 343 ASN A 345 -1 N ASN A 343 O ARG A 361 SHEET 1 D 2 ILE B 31 GLU B 32 0 SHEET 2 D 2 ILE B 340 THR B 341 1 O THR B 341 N ILE B 31 SHEET 1 E 7 ALA B 91 ASN B 93 0 SHEET 2 E 7 GLY B 238 MET B 242 -1 O ILE B 240 N ASN B 93 SHEET 3 E 7 PHE B 223 THR B 227 -1 N VAL B 224 O LEU B 241 SHEET 4 E 7 TYR B 197 ASP B 201 1 N VAL B 200 O PHE B 223 SHEET 5 E 7 LEU B 170 ALA B 173 1 N ALA B 173 O ASP B 201 SHEET 6 E 7 THR B 116 SER B 121 1 N MET B 118 O LEU B 170 SHEET 7 E 7 ASN B 142 GLY B 147 1 O TYR B 146 N GLY B 119 SHEET 1 F 4 ARG B 306 SER B 309 0 SHEET 2 F 4 VAL B 316 ASP B 320 -1 O ASP B 320 N ARG B 306 SHEET 3 F 4 GLY B 359 GLY B 363 -1 O ILE B 360 N VAL B 319 SHEET 4 F 4 ASN B 343 LYS B 344 -1 N ASN B 343 O ARG B 361 CISPEP 1 SER A 132 PRO A 133 0 -1.02 CISPEP 2 PHE B 255 PRO B 256 0 4.15 SITE 1 AC1 10 GLY A 99 SER A 100 THR A 227 HIS A 229 SITE 2 AC1 10 LYS A 230 HOH A 748 HOH A 858 GLY B 260 SITE 3 AC1 10 GLY B 261 HOH B 886 SITE 1 AC2 11 SER A 137 LYS A 139 HOH A 669 HOH A 765 SITE 2 AC2 11 HOH A 883 SER B 252 ALA B 253 ILE B 254 SITE 3 AC2 11 PHE B 255 ILE B 258 HOH B 686 SITE 1 AC3 8 PRO B 42 THR B 369 ARG B 370 VAL B 413 SITE 2 AC3 8 TYR B 414 HOH B 729 HOH B 751 HOH B 829 SITE 1 AC4 12 GLY A 260 GLY A 261 HOH A 636 SER B 98 SITE 2 AC4 12 GLY B 99 SER B 100 THR B 227 HIS B 229 SITE 3 AC4 12 LYS B 230 HOH B 674 HOH B 711 HOH B 961 CRYST1 55.280 72.580 182.120 90.00 90.00 90.00 P 21 21 21 8 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 0.018090 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013778 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005491 0.00000