HEADER LYASE 09-MAR-11 3R13 TITLE CRYSTAL STRUCTURE OF A DEOXYRIBOSE-PHOSPHATE ALDOLASE (TM_1559) FROM TITLE 2 THERMOTOGA MARITIMA AT 1.83 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYRIBOSE-PHOSPHATE ALDOLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PHOSPHODEOXYRIBOALDOLASE, DERA, DEOXYRIBOALDOLASE; COMPND 5 EC: 4.1.2.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: DEOC, TM1559, TM_1559; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DL41; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: MH1 KEYWDS TIM BETA/ALPHA-BARREL, STRUCTURAL GENOMICS, JOINT CENTER FOR KEYWDS 2 STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 4 01-FEB-23 3R13 1 REMARK SEQADV SHEET LINK REVDAT 3 08-NOV-17 3R13 1 REMARK REVDAT 2 20-JUL-11 3R13 1 HETATM REMARK REVDAT 1 30-MAR-11 3R13 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF A DEOXYRIBOSE-PHOSPHATE ALDOLASE JRNL TITL 2 (TM_1559) FROM THERMOTOGA MARITIMA AT 1.83 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 42154 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) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2116 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) : 1.83 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2932 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 164 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3978 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 259 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.80000 REMARK 3 B22 (A**2) : -0.38000 REMARK 3 B33 (A**2) : 1.17000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 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): 0.120 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.131 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4312 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2924 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5830 ; 1.432 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7160 ; 0.899 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 560 ; 5.958 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 184 ;32.897 ;23.859 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 768 ;13.512 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;17.844 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 644 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4892 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 877 ; 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): 2689 ; 1.708 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1111 ; 0.593 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4343 ; 2.822 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1623 ; 5.239 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1483 ; 8.161 ;11.000 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 205 5 REMARK 3 1 B 1 B 205 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1163 ; 0.080 ; 0.500 REMARK 3 LOOSE POSITIONAL 1 A (A): 1427 ; 0.380 ; 5.000 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1163 ; 0.750 ; 2.000 REMARK 3 LOOSE THERMAL 1 A (A**2): 1427 ; 0.910 ;10.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 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 -9 A 247 REMARK 3 ORIGIN FOR THE GROUP (A): 3.5890 23.1970 54.5460 REMARK 3 T TENSOR REMARK 3 T11: 0.0390 T22: 0.0420 REMARK 3 T33: 0.0046 T12: -0.0037 REMARK 3 T13: 0.0052 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 1.1087 L22: 0.6984 REMARK 3 L33: 0.4405 L12: 0.0296 REMARK 3 L13: 0.1435 L23: 0.0925 REMARK 3 S TENSOR REMARK 3 S11: 0.0110 S12: 0.0768 S13: -0.0031 REMARK 3 S21: -0.0077 S22: -0.0157 S23: -0.0055 REMARK 3 S31: 0.0776 S32: -0.0114 S33: 0.0047 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 : B -9 B 248 REMARK 3 ORIGIN FOR THE GROUP (A): 7.0310 43.3440 77.9150 REMARK 3 T TENSOR REMARK 3 T11: 0.0363 T22: 0.0055 REMARK 3 T33: 0.0485 T12: -0.0003 REMARK 3 T13: -0.0027 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 0.7991 L22: 0.4931 REMARK 3 L33: 0.5957 L12: 0.0736 REMARK 3 L13: 0.1150 L23: 0.1299 REMARK 3 S TENSOR REMARK 3 S11: 0.0089 S12: -0.0528 S13: 0.0172 REMARK 3 S21: 0.0881 S22: -0.0194 S23: -0.0114 REMARK 3 S31: 0.0029 S32: -0.0157 S33: 0.0105 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: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR REMARK 3 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE REMARK 3 OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO REMARK 3 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL REMARK 3 S-MET INCORPORATION. 3. THE ELECTRON DENSITY REVEALS THAT LYSINE REMARK 3 179 HAS BEEN COVALENTLY MODIFIED. IT WAS MODELED AS AN UNKNOWN REMARK 3 LIGAND (UNL). 4. ACETATE (ACT) AND GLYCEROL (GOL) MODELED IN THE REMARK 3 STRUCTURE ARE PRESENT IN CRYO/PROTEIN BUFFERS. 5. ATOM RECORD REMARK 3 CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD REMARK 3 CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 6. WATERS WERE REMARK 3 EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. REMARK 4 REMARK 4 3R13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064356. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.89194,0.97946,0.97929 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.5, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42195 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 44.677 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.55200 REMARK 200 R SYM FOR SHELL (I) : 0.55200 REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHARP, SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40.0% 1,2-PROPANEDIOL, 0.05M CALCIUM REMARK 280 ACETATE, 0.1M ACETATE PH 4.5, NANODROP, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 26.24050 REMARK 290 SMTRY3 2 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: 4470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 MSE A -11 REMARK 465 GLY A -10 REMARK 465 GLY A 248 REMARK 465 MSE B -11 REMARK 465 GLY B -10 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 LYS A -7 CG CD CE NZ REMARK 470 ARG A 5 CZ NH1 NH2 REMARK 470 GLU A 24 CG CD OE1 OE2 REMARK 470 GLU A 79 CD OE1 OE2 REMARK 470 GLU A 204 CG CD OE1 OE2 REMARK 470 LYS B -7 CG CD CE NZ REMARK 470 GLU B 79 CD OE1 OE2 REMARK 470 GLY B 248 O 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 GLU B 154 69.11 60.94 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 ACT A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 308 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 283416 RELATED DB: TARGETDB REMARK 900 RELATED ID: 3R12 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A DEOXYRIBOSE-PHOSPHATE ALDOLASE (TM_1559) REMARK 900 FROM THERMOTOGA MARITIMA AT 1.75 A RESOLUTION (APO FORM) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH. DBREF 3R13 A 1 248 UNP Q9X1P5 DEOC_THEMA 1 248 DBREF 3R13 B 1 248 UNP Q9X1P5 DEOC_THEMA 1 248 SEQADV 3R13 MSE A -11 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 GLY A -10 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 SER A -9 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 ASP A -8 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 LYS A -7 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 ILE A -6 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 HIS A -5 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 HIS A -4 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 HIS A -3 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 HIS A -2 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 HIS A -1 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 HIS A 0 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 MSE B -11 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 GLY B -10 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 SER B -9 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 ASP B -8 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 LYS B -7 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 ILE B -6 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 HIS B -5 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 HIS B -4 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 HIS B -3 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 HIS B -2 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 HIS B -1 UNP Q9X1P5 EXPRESSION TAG SEQADV 3R13 HIS B 0 UNP Q9X1P5 EXPRESSION TAG SEQRES 1 A 260 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 A 260 ILE GLU TYR ARG ILE GLU GLU ALA VAL ALA LYS TYR ARG SEQRES 3 A 260 GLU PHE TYR GLU PHE LYS PRO VAL ARG GLU SER ALA GLY SEQRES 4 A 260 ILE GLU ASP VAL LYS SER ALA ILE GLU HIS THR ASN LEU SEQRES 5 A 260 LYS PRO PHE ALA THR PRO ASP ASP ILE LYS LYS LEU CYS SEQRES 6 A 260 LEU GLU ALA ARG GLU ASN ARG PHE HIS GLY VAL CYS VAL SEQRES 7 A 260 ASN PRO CYS TYR VAL LYS LEU ALA ARG GLU GLU LEU GLU SEQRES 8 A 260 GLY THR ASP VAL LYS VAL VAL THR VAL VAL GLY PHE PRO SEQRES 9 A 260 LEU GLY ALA ASN GLU THR ARG THR LYS ALA HIS GLU ALA SEQRES 10 A 260 ILE PHE ALA VAL GLU SER GLY ALA ASP GLU ILE ASP MSE SEQRES 11 A 260 VAL ILE ASN VAL GLY MSE LEU LYS ALA LYS GLU TRP GLU SEQRES 12 A 260 TYR VAL TYR GLU ASP ILE ARG SER VAL VAL GLU SER VAL SEQRES 13 A 260 LYS GLY LYS VAL VAL LYS VAL ILE ILE GLU THR CYS TYR SEQRES 14 A 260 LEU ASP THR GLU GLU LYS ILE ALA ALA CYS VAL ILE SER SEQRES 15 A 260 LYS LEU ALA GLY ALA HIS PHE VAL LYS THR SER THR GLY SEQRES 16 A 260 PHE GLY THR GLY GLY ALA THR ALA GLU ASP VAL HIS LEU SEQRES 17 A 260 MSE LYS TRP ILE VAL GLY ASP GLU MSE GLY VAL LYS ALA SEQRES 18 A 260 SER GLY GLY ILE ARG THR PHE GLU ASP ALA VAL LYS MSE SEQRES 19 A 260 ILE MSE TYR GLY ALA ASP ARG ILE GLY THR SER SER GLY SEQRES 20 A 260 VAL LYS ILE VAL GLN GLY GLY GLU GLU ARG TYR GLY GLY SEQRES 1 B 260 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 B 260 ILE GLU TYR ARG ILE GLU GLU ALA VAL ALA LYS TYR ARG SEQRES 3 B 260 GLU PHE TYR GLU PHE LYS PRO VAL ARG GLU SER ALA GLY SEQRES 4 B 260 ILE GLU ASP VAL LYS SER ALA ILE GLU HIS THR ASN LEU SEQRES 5 B 260 LYS PRO PHE ALA THR PRO ASP ASP ILE LYS LYS LEU CYS SEQRES 6 B 260 LEU GLU ALA ARG GLU ASN ARG PHE HIS GLY VAL CYS VAL SEQRES 7 B 260 ASN PRO CYS TYR VAL LYS LEU ALA ARG GLU GLU LEU GLU SEQRES 8 B 260 GLY THR ASP VAL LYS VAL VAL THR VAL VAL GLY PHE PRO SEQRES 9 B 260 LEU GLY ALA ASN GLU THR ARG THR LYS ALA HIS GLU ALA SEQRES 10 B 260 ILE PHE ALA VAL GLU SER GLY ALA ASP GLU ILE ASP MSE SEQRES 11 B 260 VAL ILE ASN VAL GLY MSE LEU LYS ALA LYS GLU TRP GLU SEQRES 12 B 260 TYR VAL TYR GLU ASP ILE ARG SER VAL VAL GLU SER VAL SEQRES 13 B 260 LYS GLY LYS VAL VAL LYS VAL ILE ILE GLU THR CYS TYR SEQRES 14 B 260 LEU ASP THR GLU GLU LYS ILE ALA ALA CYS VAL ILE SER SEQRES 15 B 260 LYS LEU ALA GLY ALA HIS PHE VAL LYS THR SER THR GLY SEQRES 16 B 260 PHE GLY THR GLY GLY ALA THR ALA GLU ASP VAL HIS LEU SEQRES 17 B 260 MSE LYS TRP ILE VAL GLY ASP GLU MSE GLY VAL LYS ALA SEQRES 18 B 260 SER GLY GLY ILE ARG THR PHE GLU ASP ALA VAL LYS MSE SEQRES 19 B 260 ILE MSE TYR GLY ALA ASP ARG ILE GLY THR SER SER GLY SEQRES 20 B 260 VAL LYS ILE VAL GLN GLY GLY GLU GLU ARG TYR GLY GLY MODRES 3R13 MSE A 1 MET SELENOMETHIONINE MODRES 3R13 MSE A 118 MET SELENOMETHIONINE MODRES 3R13 MSE A 124 MET SELENOMETHIONINE MODRES 3R13 MSE A 197 MET SELENOMETHIONINE MODRES 3R13 MSE A 205 MET SELENOMETHIONINE MODRES 3R13 MSE A 222 MET SELENOMETHIONINE MODRES 3R13 MSE A 224 MET SELENOMETHIONINE MODRES 3R13 MSE B 1 MET SELENOMETHIONINE MODRES 3R13 MSE B 118 MET SELENOMETHIONINE MODRES 3R13 MSE B 124 MET SELENOMETHIONINE MODRES 3R13 MSE B 197 MET SELENOMETHIONINE MODRES 3R13 MSE B 205 MET SELENOMETHIONINE MODRES 3R13 MSE B 222 MET SELENOMETHIONINE MODRES 3R13 MSE B 224 MET SELENOMETHIONINE HET MSE A 1 24 HET MSE A 118 8 HET MSE A 124 8 HET MSE A 197 8 HET MSE A 205 16 HET MSE A 222 8 HET MSE A 224 8 HET MSE B 1 16 HET MSE B 118 8 HET MSE B 124 8 HET MSE B 197 8 HET MSE B 205 8 HET MSE B 222 8 HET MSE B 224 8 HET UNL A 300 6 HET ACT A 301 4 HET ACT A 302 4 HET ACT A 306 4 HET GOL A 307 6 HET ACT B 303 4 HET UNL B 300 6 HET ACT B 304 4 HET ACT B 305 4 HET GOL B 308 6 HETNAM MSE SELENOMETHIONINE HETNAM UNL UNKNOWN LIGAND HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 14(C5 H11 N O2 SE) FORMUL 4 ACT 6(C2 H3 O2 1-) FORMUL 7 GOL 2(C3 H8 O3) FORMUL 13 HOH *259(H2 O) HELIX 1 1 SER A -9 TYR A 17 1 27 HELIX 2 2 GLY A 27 ALA A 34 1 8 HELIX 3 3 THR A 45 ARG A 60 1 16 HELIX 4 4 TYR A 70 LEU A 78 1 9 HELIX 5 5 GLU A 97 SER A 111 1 15 HELIX 6 6 ASN A 121 ALA A 127 1 7 HELIX 7 7 GLU A 129 VAL A 144 1 16 HELIX 8 8 GLU A 154 LEU A 158 5 5 HELIX 9 9 ASP A 159 ALA A 173 1 15 HELIX 10 10 THR A 190 GLY A 202 1 13 HELIX 11 11 THR A 215 TYR A 225 1 11 HELIX 12 12 SER A 234 GLY A 247 1 14 HELIX 13 13 SER B -9 TYR B 17 1 27 HELIX 14 14 GLY B 27 ALA B 34 1 8 HELIX 15 15 THR B 45 ARG B 60 1 16 HELIX 16 16 TYR B 70 GLU B 79 1 10 HELIX 17 17 GLU B 97 SER B 111 1 15 HELIX 18 18 ASN B 121 ALA B 127 1 7 HELIX 19 19 GLU B 129 VAL B 144 1 16 HELIX 20 20 GLU B 154 LEU B 158 5 5 HELIX 21 21 ASP B 159 ALA B 173 1 15 HELIX 22 22 THR B 190 GLY B 202 1 13 HELIX 23 23 THR B 215 TYR B 225 1 11 HELIX 24 24 SER B 234 GLY B 247 1 14 SHEET 1 A 8 ILE A 35 ASN A 39 0 SHEET 2 A 8 GLY A 63 VAL A 66 1 O CYS A 65 N ASN A 39 SHEET 3 A 8 LYS A 84 VAL A 89 1 O VAL A 86 N VAL A 64 SHEET 4 A 8 GLU A 115 VAL A 119 1 O ASP A 117 N THR A 87 SHEET 5 A 8 VAL A 148 ILE A 152 1 O ILE A 152 N MSE A 118 SHEET 6 A 8 GLY A 206 SER A 210 1 O LYS A 208 N VAL A 178 SHEET 7 A 8 ARG A 229 THR A 232 1 O GLY A 231 N ALA A 209 SHEET 8 A 8 ILE A 35 ASN A 39 1 N THR A 38 O THR A 232 SHEET 1 B 8 ILE B 35 ASN B 39 0 SHEET 2 B 8 GLY B 63 VAL B 66 1 O GLY B 63 N HIS B 37 SHEET 3 B 8 LYS B 84 VAL B 89 1 O LYS B 84 N VAL B 64 SHEET 4 B 8 GLU B 115 VAL B 119 1 O ASP B 117 N THR B 87 SHEET 5 B 8 VAL B 148 ILE B 152 1 O ILE B 152 N MSE B 118 SHEET 6 B 8 GLY B 206 SER B 210 1 O LYS B 208 N VAL B 178 SHEET 7 B 8 ARG B 229 THR B 232 1 O GLY B 231 N ALA B 209 SHEET 8 B 8 ILE B 35 ASN B 39 1 N GLU B 36 O ILE B 230 LINK C HIS A 0 N AMSE A 1 1555 1555 1.33 LINK C HIS A 0 N BMSE A 1 1555 1555 1.34 LINK C HIS A 0 N CMSE A 1 1555 1555 1.34 LINK C AMSE A 1 N ILE A 2 1555 1555 1.34 LINK C BMSE A 1 N ILE A 2 1555 1555 1.33 LINK C CMSE A 1 N ILE A 2 1555 1555 1.33 LINK C ASP A 117 N MSE A 118 1555 1555 1.34 LINK C MSE A 118 N VAL A 119 1555 1555 1.35 LINK C GLY A 123 N MSE A 124 1555 1555 1.32 LINK C MSE A 124 N LEU A 125 1555 1555 1.34 LINK NZ LYS A 179 C1' UNL A 300 1555 1555 1.45 LINK C LEU A 196 N MSE A 197 1555 1555 1.33 LINK C MSE A 197 N LYS A 198 1555 1555 1.32 LINK C GLU A 204 N AMSE A 205 1555 1555 1.32 LINK C GLU A 204 N BMSE A 205 1555 1555 1.34 LINK C AMSE A 205 N GLY A 206 1555 1555 1.32 LINK C BMSE A 205 N GLY A 206 1555 1555 1.33 LINK C LYS A 221 N MSE A 222 1555 1555 1.32 LINK C MSE A 222 N ILE A 223 1555 1555 1.33 LINK C ILE A 223 N MSE A 224 1555 1555 1.33 LINK C MSE A 224 N TYR A 225 1555 1555 1.33 LINK C AHIS B 0 N AMSE B 1 1555 1555 1.33 LINK C BHIS B 0 N BMSE B 1 1555 1555 1.33 LINK C AMSE B 1 N ILE B 2 1555 1555 1.33 LINK C BMSE B 1 N ILE B 2 1555 1555 1.34 LINK C ASP B 117 N MSE B 118 1555 1555 1.34 LINK C MSE B 118 N VAL B 119 1555 1555 1.32 LINK C GLY B 123 N MSE B 124 1555 1555 1.33 LINK C MSE B 124 N LEU B 125 1555 1555 1.32 LINK NZ LYS B 179 C1' UNL B 300 1555 1555 1.47 LINK C LEU B 196 N MSE B 197 1555 1555 1.33 LINK C MSE B 197 N LYS B 198 1555 1555 1.34 LINK C GLU B 204 N MSE B 205 1555 1555 1.32 LINK C MSE B 205 N GLY B 206 1555 1555 1.33 LINK C LYS B 221 N MSE B 222 1555 1555 1.34 LINK C MSE B 222 N ILE B 223 1555 1555 1.33 LINK C ILE B 223 N MSE B 224 1555 1555 1.32 LINK C MSE B 224 N TYR B 225 1555 1555 1.33 CISPEP 1 PHE A 91 PRO A 92 0 2.22 CISPEP 2 PHE B 91 PRO B 92 0 1.85 SITE 1 AC1 3 TYR A 13 ARG A 14 TYR A 17 SITE 1 AC2 1 TYR A 157 SITE 1 AC3 1 ILE A 200 SITE 1 AC4 8 GLY A 212 ILE A 213 ARG A 214 THR A 232 SITE 2 AC4 8 SER A 233 SER A 234 HOH A 320 HOH A 400 SITE 1 AC5 1 CYS B 69 SITE 1 AC6 2 ARG B 14 GLU B 161 SITE 1 AC7 2 GLY B 187 GLY B 188 SITE 1 AC8 7 ILE B 213 ARG B 214 THR B 232 SER B 233 SITE 2 AC8 7 SER B 234 HOH B 331 HOH B 420 CRYST1 53.904 52.481 85.462 90.00 95.59 90.00 P 1 21 1 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 0.018551 0.000000 0.001816 0.00000 SCALE2 0.000000 0.019055 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011757 0.00000