HEADER ISOMERASE 22-SEP-11 3TWZ TITLE PHOSPHORYLATED BACILLUS CEREUS PHOSPHOPENTOMUTASE IN SPACE GROUP TITLE 2 P212121 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOPENTOMUTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHODEOXYRIBOMUTASE; COMPND 5 EC: 5.4.2.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 1396; SOURCE 4 GENE: DEOB, BC_4087; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALKALINE PHOSPHATASE SUPERFAMILY, PHOSPHORYLATION, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.P.PANOSIAN,D.P.NANNEMAN,B.O.BACHMANN,T.M.IVERSON REVDAT 3 30-OCT-24 3TWZ 1 REMARK SEQADV LINK REVDAT 2 21-MAR-12 3TWZ 1 JRNL REVDAT 1 29-FEB-12 3TWZ 0 JRNL AUTH T.M.IVERSON,T.D.PANOSIAN,W.R.BIRMINGHAM,D.P.NANNEMANN, JRNL AUTH 2 B.O.BACHMANN JRNL TITL MOLECULAR DIFFERENCES BETWEEN A MUTASE AND A PHOSPHATASE: JRNL TITL 2 INVESTIGATIONS OF THE ACTIVATION STEP IN BACILLUS CEREUS JRNL TITL 3 PHOSPHOPENTOMUTASE. JRNL REF BIOCHEMISTRY V. 51 1964 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 22329805 JRNL DOI 10.1021/BI201761H REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 45485 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2428 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2118 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE SET COUNT : 119 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3069 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 443 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.50000 REMARK 3 B22 (A**2) : -2.17000 REMARK 3 B33 (A**2) : -1.33000 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): 0.103 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.066 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.439 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3192 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4324 ; 1.040 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 404 ; 5.344 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 152 ;36.851 ;25.132 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 569 ;12.823 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;18.489 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 468 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2450 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1973 ; 0.322 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3188 ; 0.625 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1219 ; 1.176 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1134 ; 2.018 ; 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 79 REMARK 3 ORIGIN FOR THE GROUP (A): -14.3990 3.9821 -21.1663 REMARK 3 T TENSOR REMARK 3 T11: 0.0310 T22: 0.0902 REMARK 3 T33: 0.0770 T12: -0.0024 REMARK 3 T13: 0.0239 T23: 0.0127 REMARK 3 L TENSOR REMARK 3 L11: 1.7415 L22: 1.4284 REMARK 3 L33: 1.9471 L12: -0.4628 REMARK 3 L13: 0.7027 L23: -0.6255 REMARK 3 S TENSOR REMARK 3 S11: -0.0288 S12: -0.1165 S13: -0.1339 REMARK 3 S21: 0.1123 S22: 0.1071 S23: 0.2312 REMARK 3 S31: 0.1209 S32: -0.2838 S33: -0.0783 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 80 A 158 REMARK 3 ORIGIN FOR THE GROUP (A): -0.8911 16.6180 -46.7859 REMARK 3 T TENSOR REMARK 3 T11: 0.0910 T22: 0.1244 REMARK 3 T33: 0.1259 T12: -0.0207 REMARK 3 T13: 0.0067 T23: -0.0123 REMARK 3 L TENSOR REMARK 3 L11: 0.8752 L22: 0.0247 REMARK 3 L33: 4.6099 L12: 0.0175 REMARK 3 L13: -1.6796 L23: 0.0254 REMARK 3 S TENSOR REMARK 3 S11: -0.1389 S12: 0.2599 S13: -0.0862 REMARK 3 S21: -0.0437 S22: -0.0078 S23: 0.0016 REMARK 3 S31: 0.1776 S32: -0.3114 S33: 0.1467 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 159 A 215 REMARK 3 ORIGIN FOR THE GROUP (A): 9.0357 14.7920 -47.5861 REMARK 3 T TENSOR REMARK 3 T11: 0.0754 T22: 0.1646 REMARK 3 T33: 0.0832 T12: 0.0180 REMARK 3 T13: 0.0372 T23: 0.0463 REMARK 3 L TENSOR REMARK 3 L11: 4.2657 L22: 3.3675 REMARK 3 L33: 6.3958 L12: -1.3269 REMARK 3 L13: -1.9868 L23: 2.4812 REMARK 3 S TENSOR REMARK 3 S11: -0.3240 S12: -0.2513 S13: -0.2080 REMARK 3 S21: 0.3241 S22: 0.1417 S23: -0.0894 REMARK 3 S31: 0.5087 S32: 0.5949 S33: 0.1823 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 216 A 392 REMARK 3 ORIGIN FOR THE GROUP (A): -1.5442 7.4962 -21.5329 REMARK 3 T TENSOR REMARK 3 T11: 0.0055 T22: 0.0299 REMARK 3 T33: 0.0189 T12: 0.0077 REMARK 3 T13: 0.0028 T23: 0.0075 REMARK 3 L TENSOR REMARK 3 L11: 1.4800 L22: 1.8342 REMARK 3 L33: 1.1428 L12: 0.0512 REMARK 3 L13: 0.2009 L23: -0.3646 REMARK 3 S TENSOR REMARK 3 S11: -0.0295 S12: -0.0425 S13: -0.0345 REMARK 3 S21: 0.0685 S22: 0.0359 S23: -0.0752 REMARK 3 S31: -0.0002 S32: 0.0400 S33: -0.0064 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3TWZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068024. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 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-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47942 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 91.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.4 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 125 MM MANGANESE CHLORIDE, 1.8 M REMARK 280 AMMONIUM CITRATE, PH 7.2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 34.33750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.68700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.29050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.68700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.33750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.29050 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 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 GLY A -4 REMARK 465 SER A -3 REMARK 465 HIS A -2 REMARK 465 MET A -1 REMARK 465 ALA A 0 REMARK 465 SER A 1 REMARK 465 ASN A 2 REMARK 465 LYS A 394 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 393 CG CD CE 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 LYS A 393 CB LYS A 393 CG -0.648 REMARK 500 LYS A 393 CE LYS A 393 NZ -0.343 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 LYS A 393 CA - CB - CG ANGL. DEV. = 27.3 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 ASP A 32 91.49 -161.10 REMARK 500 THR A 74 -173.79 -177.33 REMARK 500 SER A 154 -156.71 -118.04 REMARK 500 TYR A 189 57.65 -154.97 REMARK 500 ASN A 205 56.18 -149.60 REMARK 500 HIS A 328 -174.35 -177.48 REMARK 500 ASN A 330 72.78 -160.46 REMARK 500 LEU A 392 44.30 -76.00 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 MN A 396 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 ASP A 13 OD2 56.5 REMARK 620 3 TPO A 85 OG1 127.7 108.6 REMARK 620 4 ASP A 327 OD2 118.3 87.0 109.3 REMARK 620 5 HIS A 328 NE2 97.5 150.5 98.3 95.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 395 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TPO A 85 O1P REMARK 620 2 ASP A 156 OD2 83.1 REMARK 620 3 ASP A 156 OD1 87.5 51.6 REMARK 620 4 ASP A 286 OD1 89.7 142.5 91.6 REMARK 620 5 HIS A 291 NE2 171.3 88.5 88.9 98.3 REMARK 620 6 HIS A 339 NE2 83.8 92.5 143.8 123.3 94.5 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 MN A 395 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 396 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TX0 RELATED DB: PDB REMARK 900 UNPHOSPHORYLATED BACILLUS CEREUS PHOSPHOPENTOMUTASE IN A P212121 REMARK 900 CRYSTAL FORM DBREF 3TWZ A 2 394 UNP Q818Z9 DEOB_BACCR 2 394 SEQADV 3TWZ GLY A -4 UNP Q818Z9 EXPRESSION TAG SEQADV 3TWZ SER A -3 UNP Q818Z9 EXPRESSION TAG SEQADV 3TWZ HIS A -2 UNP Q818Z9 EXPRESSION TAG SEQADV 3TWZ MET A -1 UNP Q818Z9 EXPRESSION TAG SEQADV 3TWZ ALA A 0 UNP Q818Z9 EXPRESSION TAG SEQADV 3TWZ SER A 1 UNP Q818Z9 EXPRESSION TAG SEQRES 1 A 399 GLY SER HIS MET ALA SER ASN LYS TYR LYS ARG ILE PHE SEQRES 2 A 399 LEU VAL VAL MET ASP SER VAL GLY ILE GLY GLU ALA PRO SEQRES 3 A 399 ASP ALA GLU GLN PHE GLY ASP LEU GLY SER ASP THR ILE SEQRES 4 A 399 GLY HIS ILE ALA GLU HIS MET ASN GLY LEU GLN MET PRO SEQRES 5 A 399 ASN MET VAL LYS LEU GLY LEU GLY ASN ILE ARG GLU MET SEQRES 6 A 399 LYS GLY ILE SER LYS VAL GLU LYS PRO LEU GLY TYR TYR SEQRES 7 A 399 THR LYS MET GLN GLU LYS SER THR GLY LYS ASP TPO MET SEQRES 8 A 399 THR GLY HIS TRP GLU ILE MET GLY LEU TYR ILE ASP THR SEQRES 9 A 399 PRO PHE GLN VAL PHE PRO GLU GLY PHE PRO LYS GLU LEU SEQRES 10 A 399 LEU ASP GLU LEU GLU GLU LYS THR GLY ARG LYS ILE ILE SEQRES 11 A 399 GLY ASN LYS PRO ALA SER GLY THR GLU ILE LEU ASP GLU SEQRES 12 A 399 LEU GLY GLN GLU GLN MET GLU THR GLY SER LEU ILE VAL SEQRES 13 A 399 TYR THR SER ALA ASP SER VAL LEU GLN ILE ALA ALA HIS SEQRES 14 A 399 GLU GLU VAL VAL PRO LEU ASP GLU LEU TYR LYS ILE CYS SEQRES 15 A 399 LYS ILE ALA ARG GLU LEU THR LEU ASP GLU LYS TYR MET SEQRES 16 A 399 VAL GLY ARG VAL ILE ALA ARG PRO PHE VAL GLY GLU PRO SEQRES 17 A 399 GLY ASN PHE THR ARG THR PRO ASN ARG HIS ASP TYR ALA SEQRES 18 A 399 LEU LYS PRO PHE GLY ARG THR VAL MET ASN GLU LEU LYS SEQRES 19 A 399 ASP SER ASP TYR ASP VAL ILE ALA ILE GLY LYS ILE SER SEQRES 20 A 399 ASP ILE TYR ASP GLY GLU GLY VAL THR GLU SER LEU ARG SEQRES 21 A 399 THR LYS SER ASN MET ASP GLY MET ASP LYS LEU VAL ASP SEQRES 22 A 399 THR LEU ASN MET ASP PHE THR GLY LEU SER PHE LEU ASN SEQRES 23 A 399 LEU VAL ASP PHE ASP ALA LEU PHE GLY HIS ARG ARG ASP SEQRES 24 A 399 PRO GLN GLY TYR GLY GLU ALA LEU GLN GLU TYR ASP ALA SEQRES 25 A 399 ARG LEU PRO GLU VAL PHE ALA LYS LEU LYS GLU ASP ASP SEQRES 26 A 399 LEU LEU LEU ILE THR ALA ASP HIS GLY ASN ASP PRO ILE SEQRES 27 A 399 HIS PRO GLY THR ASP HIS THR ARG GLU TYR VAL PRO LEU SEQRES 28 A 399 LEU ALA TYR SER PRO SER MET LYS GLU GLY GLY GLN GLU SEQRES 29 A 399 LEU PRO LEU ARG GLN THR PHE ALA ASP ILE GLY ALA THR SEQRES 30 A 399 VAL ALA GLU ASN PHE GLY VAL LYS MET PRO GLU TYR GLY SEQRES 31 A 399 THR SER PHE LEU ASN GLU LEU LYS LYS MODRES 3TWZ TPO A 85 THR PHOSPHOTHREONINE HET TPO A 85 11 HET MN A 395 1 HET MN A 396 1 HETNAM TPO PHOSPHOTHREONINE HETNAM MN MANGANESE (II) ION HETSYN TPO PHOSPHONOTHREONINE FORMUL 1 TPO C4 H10 N O6 P FORMUL 2 MN 2(MN 2+) FORMUL 4 HOH *443(H2 O) HELIX 1 1 ASP A 22 GLY A 27 5 6 HELIX 2 2 ASP A 32 MET A 41 1 10 HELIX 3 3 MET A 46 GLY A 53 1 8 HELIX 4 4 GLY A 53 ARG A 58 1 6 HELIX 5 5 ASP A 84 MET A 93 1 10 HELIX 6 6 PRO A 109 GLY A 121 1 13 HELIX 7 7 SER A 131 GLY A 147 1 17 HELIX 8 8 PRO A 169 THR A 184 1 16 HELIX 9 9 ASP A 186 MET A 190 5 5 HELIX 10 10 THR A 223 SER A 231 1 9 HELIX 11 11 LYS A 240 TYR A 245 1 6 HELIX 12 12 SER A 258 ASN A 271 1 14 HELIX 13 13 VAL A 283 PHE A 289 1 7 HELIX 14 14 ASP A 294 LEU A 316 1 23 HELIX 15 15 PHE A 366 GLY A 378 1 13 HELIX 16 16 PHE A 388 LEU A 392 5 5 SHEET 1 A 7 TYR A 72 MET A 76 0 SHEET 2 A 7 VAL A 344 TYR A 349 -1 O VAL A 344 N MET A 76 SHEET 3 A 7 ASP A 320 THR A 325 -1 N LEU A 322 O TYR A 349 SHEET 4 A 7 ARG A 6 MET A 12 1 N VAL A 10 O LEU A 323 SHEET 5 A 7 GLY A 276 LEU A 282 1 O LEU A 280 N LEU A 9 SHEET 6 A 7 ASP A 234 ILE A 238 1 N ILE A 238 O PHE A 279 SHEET 7 A 7 GLU A 252 LEU A 254 1 O LEU A 254 N ALA A 237 SHEET 1 B 5 ILE A 124 PRO A 129 0 SHEET 2 B 5 LEU A 149 THR A 153 1 O LEU A 149 N ILE A 125 SHEET 3 B 5 VAL A 158 HIS A 164 -1 O GLN A 160 N TYR A 152 SHEET 4 B 5 ARG A 193 GLU A 202 1 O ARG A 197 N ILE A 161 SHEET 5 B 5 ASN A 205 ARG A 208 -1 O ASN A 205 N GLU A 202 SHEET 1 C 5 ILE A 124 PRO A 129 0 SHEET 2 C 5 LEU A 149 THR A 153 1 O LEU A 149 N ILE A 125 SHEET 3 C 5 VAL A 158 HIS A 164 -1 O GLN A 160 N TYR A 152 SHEET 4 C 5 ARG A 193 GLU A 202 1 O ARG A 197 N ILE A 161 SHEET 5 C 5 HIS A 213 ALA A 216 -1 O HIS A 213 N ALA A 196 LINK C ASP A 84 N TPO A 85 1555 1555 1.34 LINK C TPO A 85 N MET A 86 1555 1555 1.33 LINK OD1 ASP A 13 MN MN A 396 1555 1555 2.09 LINK OD2 ASP A 13 MN MN A 396 1555 1555 2.51 LINK O1P TPO A 85 MN MN A 395 1555 1555 1.86 LINK OG1 TPO A 85 MN MN A 396 1555 1555 2.22 LINK OD2 ASP A 156 MN MN A 395 1555 1555 2.17 LINK OD1 ASP A 156 MN MN A 395 1555 1555 2.73 LINK OD1 ASP A 286 MN MN A 395 1555 1555 2.10 LINK NE2 HIS A 291 MN MN A 395 1555 1555 2.16 LINK OD2 ASP A 327 MN MN A 396 1555 1555 2.13 LINK NE2 HIS A 328 MN MN A 396 1555 1555 2.20 LINK NE2 HIS A 339 MN MN A 395 1555 1555 2.21 SITE 1 AC1 5 TPO A 85 ASP A 156 ASP A 286 HIS A 291 SITE 2 AC1 5 HIS A 339 SITE 1 AC2 4 ASP A 13 TPO A 85 ASP A 327 HIS A 328 CRYST1 68.675 76.581 97.374 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 0.014561 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013058 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010270 0.00000