HEADER LYASE 01-SEP-20 7JZ9 TITLE DIHYDRODIPICOLINATE SYNTHASE S48F WITH PYRUVATE AND SUCCINIC SEMI- TITLE 2 ALDEHYDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-HYDROXY-TETRAHYDRODIPICOLINATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HTPA SYNTHASE; COMPND 5 EC: 4.3.3.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: DAPA, A6V01_06140, A8C65_04230, ACU57_04510, AM464_03890, SOURCE 5 AML07_10805, APZ14_05880, AUQ13_12840, AUS26_08890, AW106_01920, SOURCE 6 BANRA_01022, BANRA_04600, BMA87_04055, BUE81_00170, BVCMS2454_00575, SOURCE 7 BVCMSKSP026_00126, BVCMSSINP011_00590, BW690_08395, BZL31_19835, SOURCE 8 C5N07_10510, C9306_12515, C9Z39_22035, C9Z89_01665, CG692_24655, SOURCE 9 CI693_08805, CIG45_08195, COD30_00655, D2185_06295, D3821_11825, SOURCE 10 D4638_04510, D4718_03620, D5H35_00590, D6004_00600, D9610_05430, SOURCE 11 D9D44_02140, D9I18_08280, D9J52_02245, D9S45_15015, DAH30_02905, SOURCE 12 DAH32_09095, DIV22_31750, DJ503_11770, DL326_03925, DL530_01595, SOURCE 13 DL800_18800, DLW60_01905, DMY83_09445, DNW42_05980, DQF71_00895, SOURCE 14 DS143_00895, DT034_06790, DTL43_01515, DVB38_05855, E2119_05140, SOURCE 15 E2134_09475, E2135_00560, E2855_03226, E2863_03133, E5P22_02280, SOURCE 16 E5S42_08940, EAI42_12285, EAI52_02575, EAM59_02025, EAN70_00660, SOURCE 17 EBM08_03910, EC3234A_44C00840, EC95NR1_01697, ECTO6_01408, SOURCE 18 ED307_17520, ED600_00625, EEP23_23010, EG599_00615, EH412_01980, SOURCE 19 EHJ36_02055, EI028_07440, EIZ93_19645, EKI52_22350, EL75_1173, SOURCE 20 EL79_1184, EL80_1189, EPT01_15155, ERS150876_00779, EYD11_06580, SOURCE 21 F1E19_01790, F7F00_00605, F7F23_09350, F7F26_01975, FQR64_06700, SOURCE 22 GHR40_11105, GKF74_08320, GKF86_10525, GKF89_17025, GP666_02180, SOURCE 23 GP935_11985, GQA06_13610, GQE30_13075, GQE34_24640, GQE51_05930, SOURCE 24 GRW80_06100, NCTC10963_01382, NCTC11126_06127, NCTC11341_00817, SOURCE 25 NCTC13216_00544, NCTC8960_04113, NCTC9045_01668, NCTC9062_01738, SOURCE 26 NCTC9962_06536, RK56_024520, SAMEA3472047_03904, SAMEA3484427_00338, SOURCE 27 SAMEA3484429_00447, SAMEA3752559_00798, SAMEA3753300_00971, SOURCE 28 SK85_02727; SOURCE 29 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 30 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENZYME, ALLOSTERY, LYSINE BIOSYNTHESIS, DHDPS, SUBSTRATE COMPLEX, KEYWDS 2 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR A.J.BOARD,R.C.J.DOBSON REVDAT 3 15-NOV-23 7JZ9 1 LINK REVDAT 2 18-OCT-23 7JZ9 1 REMARK REVDAT 1 22-SEP-21 7JZ9 0 JRNL AUTH A.J.BOARD,R.C.J.DOBSON JRNL TITL MAPPING THE UNCHARTED WATER CHANNEL OF DHDPS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 78999 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4156 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) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5796 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 311 REMARK 3 BIN FREE R VALUE : 0.2060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4319 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 649 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.078 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.080 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.650 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4467 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4236 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6087 ; 2.218 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9788 ; 1.206 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 601 ; 6.328 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 162 ;34.443 ;23.827 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 714 ;13.147 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;18.446 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 746 ; 0.152 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4988 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 841 ; 0.002 ; 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): 2359 ; 2.059 ; 1.787 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2358 ; 2.050 ; 1.786 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2945 ; 2.603 ; 2.667 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2946 ; 2.609 ; 2.668 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2108 ; 3.173 ; 2.073 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2108 ; 3.128 ; 2.073 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3133 ; 4.461 ; 2.990 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5289 ; 5.946 ;24.119 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5290 ; 5.947 ;24.129 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 7JZ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1000251595. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 294.15 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95369 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83589 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 33.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32900 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: PDB ENTRY 1YXC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: GLUCOPYRANOSIDE, POTASSIUM PHOSPHATE REMARK 280 DIBASIC, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294.15K 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 36.69367 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 73.38733 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 73.38733 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 36.69367 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 36.69367 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 682 LIES ON A SPECIAL POSITION. 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 MET A 1 CB CG SD CE REMARK 470 LYS A 26 CE NZ REMARK 470 MET A 61 CE REMARK 470 ASP A 94 CG OD1 OD2 REMARK 470 GLU A 146 CD OE1 OE2 REMARK 470 LYS A 153 CE NZ REMARK 470 LYS A 155 CD CE NZ REMARK 470 GLU A 175 CD OE1 OE2 REMARK 470 ASP A 179 CG OD1 OD2 REMARK 470 ARG A 212 CD NE CZ NH1 NH2 REMARK 470 GLN A 216 CG CD OE1 NE2 REMARK 470 LYS A 219 CE NZ REMARK 470 GLU A 228 CG CD OE1 OE2 REMARK 470 GLN A 234 OE1 NE2 REMARK 470 LYS A 257 CE NZ REMARK 470 ARG A 279 CZ NH1 NH2 REMARK 470 GLU A 280 CG CD OE1 OE2 REMARK 470 LYS A 287 CD CE NZ REMARK 470 GLU B 15 CD OE1 OE2 REMARK 470 LYS B 16 CD CE NZ REMARK 470 MET B 61 CE REMARK 470 GLU B 84 CD OE1 OE2 REMARK 470 ASP B 94 CG OD1 OD2 REMARK 470 GLU B 124 CD OE1 OE2 REMARK 470 GLU B 146 CD OE1 OE2 REMARK 470 LYS B 153 CE NZ REMARK 470 LYS B 155 CD CE NZ REMARK 470 GLU B 175 CD OE1 OE2 REMARK 470 ASP B 179 CG OD1 OD2 REMARK 470 GLN B 234 CD OE1 NE2 REMARK 470 LYS B 257 CE NZ REMARK 470 GLU B 280 CG CD OE1 OE2 REMARK 470 LYS B 287 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG1 THR A 272 O HOH A 401 1.65 REMARK 500 NH1 ARG B 235 O HOH B 401 1.80 REMARK 500 O HOH A 664 O HOH A 676 1.89 REMARK 500 O HOH B 401 O HOH B 609 1.99 REMARK 500 O HOH A 507 O HOH A 565 2.07 REMARK 500 O HOH B 440 O HOH B 625 2.09 REMARK 500 NH1 ARG B 230 O HOH B 402 2.11 REMARK 500 OG SER A 41 O HOH A 402 2.11 REMARK 500 O HOH B 531 O HOH B 604 2.13 REMARK 500 O HOH B 501 O HOH B 730 2.14 REMARK 500 O HOH B 408 O HOH B 698 2.14 REMARK 500 O HOH B 559 O HOH B 651 2.16 REMARK 500 O HOH A 573 O HOH A 632 2.16 REMARK 500 OG1 THR B 272 O HOH B 403 2.17 REMARK 500 OD1 ASP B 58 O HOH B 404 2.18 REMARK 500 O HOH B 660 O HOH B 673 2.18 REMARK 500 O HOH B 685 O HOH B 691 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 628 O HOH A 642 6555 1.83 REMARK 500 O HOH A 628 O HOH A 628 6555 2.02 REMARK 500 O HOH A 597 O HOH B 494 3654 2.08 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 GLU A 84 CG GLU A 84 CD 0.093 REMARK 500 ILE A 160 C VPV A 161 N 0.187 REMARK 500 VPV A 161 C GLU A 162 N 0.158 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 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 21 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 TYR A 133 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ILE A 160 O - C - N ANGL. DEV. = -11.4 DEGREES REMARK 500 ARG A 230 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 235 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 268 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 150 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 169 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 235 CG - CD - NE ANGL. DEV. = 13.6 DEGREES REMARK 500 ARG B 235 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ASP B 276 CB - CG - OD1 ANGL. DEV. = 5.5 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 TYR A 107 -51.60 79.40 REMARK 500 TYR B 107 -51.17 79.61 REMARK 500 VAL B 135 77.05 -150.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 696 DISTANCE = 5.81 ANGSTROMS 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 K A 302 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 80 OD1 REMARK 620 2 GLU A 84 OE2 86.3 REMARK 620 3 HOH A 608 O 133.4 67.6 REMARK 620 4 ALA B 49 O 83.5 118.5 77.0 REMARK 620 5 GOL B 302 O3 79.6 98.4 139.7 138.2 REMARK 620 6 HOH B 479 O 134.0 137.6 73.2 65.3 101.2 REMARK 620 7 HOH B 533 O 73.3 147.1 144.4 85.2 53.3 71.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 301 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 152 O REMARK 620 2 VAL A 154 O 82.6 REMARK 620 3 LYS A 155 O 147.7 68.5 REMARK 620 4 ILE A 157 O 95.6 83.6 95.1 REMARK 620 5 HOH A 617 O 75.0 92.3 91.6 170.2 REMARK 620 6 HOH A 646 O 93.7 173.0 116.5 90.9 92.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 301 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 152 O REMARK 620 2 VAL B 154 O 83.1 REMARK 620 3 LYS B 155 O 147.1 67.9 REMARK 620 4 ILE B 157 O 97.9 81.6 93.0 REMARK 620 5 HOH B 645 O 98.3 178.2 111.0 97.1 REMARK 620 6 HOH B 665 O 80.7 91.3 84.7 172.9 89.9 REMARK 620 N 1 2 3 4 5 DBREF1 7JZ9 A 1 292 UNP A0A066Q637_ECOLX DBREF2 7JZ9 A A0A066Q637 1 292 DBREF1 7JZ9 B 1 292 UNP A0A066Q637_ECOLX DBREF2 7JZ9 B A0A066Q637 1 292 SEQADV 7JZ9 PHE A 48 UNP A0A066Q63 SER 48 ENGINEERED MUTATION SEQADV 7JZ9 PHE B 48 UNP A0A066Q63 SER 48 ENGINEERED MUTATION SEQRES 1 A 292 MET PHE THR GLY SER ILE VAL ALA ILE VAL THR PRO MET SEQRES 2 A 292 ASP GLU LYS GLY ASN VAL CYS ARG ALA SER LEU LYS LYS SEQRES 3 A 292 LEU ILE ASP TYR HIS VAL ALA SER GLY THR SER ALA ILE SEQRES 4 A 292 VAL SER VAL GLY THR THR GLY GLU PHE ALA THR LEU ASN SEQRES 5 A 292 HIS ASP GLU HIS ALA ASP VAL VAL MET MET THR LEU ASP SEQRES 6 A 292 LEU ALA ASP GLY ARG ILE PRO VAL ILE ALA GLY THR GLY SEQRES 7 A 292 ALA ASN ALA THR ALA GLU ALA ILE SER LEU THR GLN ARG SEQRES 8 A 292 PHE ASN ASP SER GLY ILE VAL GLY CYS LEU THR VAL THR SEQRES 9 A 292 PRO TYR TYR ASN ARG PRO SER GLN GLU GLY LEU TYR GLN SEQRES 10 A 292 HIS PHE LYS ALA ILE ALA GLU HIS THR ASP LEU PRO GLN SEQRES 11 A 292 ILE LEU TYR ASN VAL PRO SER ARG THR GLY CYS ASP LEU SEQRES 12 A 292 LEU PRO GLU THR VAL GLY ARG LEU ALA LYS VAL LYS ASN SEQRES 13 A 292 ILE ILE GLY ILE VPV GLU ALA THR GLY ASN LEU THR ARG SEQRES 14 A 292 VAL ASN GLN ILE LYS GLU LEU VAL SER ASP ASP PHE VAL SEQRES 15 A 292 LEU LEU SER GLY ASP ASP ALA SER ALA LEU ASP PHE MET SEQRES 16 A 292 GLN LEU GLY GLY HIS GLY VAL ILE SER VAL THR ALA ASN SEQRES 17 A 292 VAL ALA ALA ARG ASP MET ALA GLN MET CYS LYS LEU ALA SEQRES 18 A 292 ALA GLU GLY HIS PHE ALA GLU ALA ARG VAL ILE ASN GLN SEQRES 19 A 292 ARG LEU MET PRO LEU HIS ASN LYS LEU PHE VAL GLU PRO SEQRES 20 A 292 ASN PRO ILE PRO VAL LYS TRP ALA CYS LYS GLU LEU GLY SEQRES 21 A 292 LEU VAL ALA THR ASP THR LEU ARG LEU PRO MET THR PRO SEQRES 22 A 292 ILE THR ASP SER GLY ARG GLU THR VAL ARG ALA ALA LEU SEQRES 23 A 292 LYS HIS ALA GLY LEU LEU SEQRES 1 B 292 MET PHE THR GLY SER ILE VAL ALA ILE VAL THR PRO MET SEQRES 2 B 292 ASP GLU LYS GLY ASN VAL CYS ARG ALA SER LEU LYS LYS SEQRES 3 B 292 LEU ILE ASP TYR HIS VAL ALA SER GLY THR SER ALA ILE SEQRES 4 B 292 VAL SER VAL GLY THR THR GLY GLU PHE ALA THR LEU ASN SEQRES 5 B 292 HIS ASP GLU HIS ALA ASP VAL VAL MET MET THR LEU ASP SEQRES 6 B 292 LEU ALA ASP GLY ARG ILE PRO VAL ILE ALA GLY THR GLY SEQRES 7 B 292 ALA ASN ALA THR ALA GLU ALA ILE SER LEU THR GLN ARG SEQRES 8 B 292 PHE ASN ASP SER GLY ILE VAL GLY CYS LEU THR VAL THR SEQRES 9 B 292 PRO TYR TYR ASN ARG PRO SER GLN GLU GLY LEU TYR GLN SEQRES 10 B 292 HIS PHE LYS ALA ILE ALA GLU HIS THR ASP LEU PRO GLN SEQRES 11 B 292 ILE LEU TYR ASN VAL PRO SER ARG THR GLY CYS ASP LEU SEQRES 12 B 292 LEU PRO GLU THR VAL GLY ARG LEU ALA LYS VAL LYS ASN SEQRES 13 B 292 ILE ILE GLY ILE VPV GLU ALA THR GLY ASN LEU THR ARG SEQRES 14 B 292 VAL ASN GLN ILE LYS GLU LEU VAL SER ASP ASP PHE VAL SEQRES 15 B 292 LEU LEU SER GLY ASP ASP ALA SER ALA LEU ASP PHE MET SEQRES 16 B 292 GLN LEU GLY GLY HIS GLY VAL ILE SER VAL THR ALA ASN SEQRES 17 B 292 VAL ALA ALA ARG ASP MET ALA GLN MET CYS LYS LEU ALA SEQRES 18 B 292 ALA GLU GLY HIS PHE ALA GLU ALA ARG VAL ILE ASN GLN SEQRES 19 B 292 ARG LEU MET PRO LEU HIS ASN LYS LEU PHE VAL GLU PRO SEQRES 20 B 292 ASN PRO ILE PRO VAL LYS TRP ALA CYS LYS GLU LEU GLY SEQRES 21 B 292 LEU VAL ALA THR ASP THR LEU ARG LEU PRO MET THR PRO SEQRES 22 B 292 ILE THR ASP SER GLY ARG GLU THR VAL ARG ALA ALA LEU SEQRES 23 B 292 LYS HIS ALA GLY LEU LEU MODRES 7JZ9 VPV A 161 LYS MODIFIED RESIDUE MODRES 7JZ9 VPV B 161 LYS MODIFIED RESIDUE HET VPV A 161 21 HET VPV B 161 21 HET K A 301 1 HET K A 302 1 HET K B 301 1 HET GOL B 302 6 HETNAM VPV (2E,4R)-2-{[(5S)-5-AMINO-5-CARBOXYPENTYL]IMINO}-4- HETNAM 2 VPV HYDROXYHEPTANEDIOIC ACID HETNAM K POTASSIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 VPV 2(C13 H22 N2 O7) FORMUL 3 K 3(K 1+) FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *649(H2 O) HELIX 1 AA1 CYS A 20 GLY A 35 1 16 HELIX 2 AA2 GLU A 47 LEU A 51 5 5 HELIX 3 AA3 ASN A 52 ASP A 68 1 17 HELIX 4 AA4 ALA A 81 ARG A 91 1 11 HELIX 5 AA5 SER A 111 HIS A 125 1 15 HELIX 6 AA6 VAL A 135 GLY A 140 1 6 HELIX 7 AA7 LEU A 144 ALA A 152 1 9 HELIX 8 AA8 THR A 168 GLU A 175 1 8 HELIX 9 AA9 ASP A 187 ALA A 189 5 3 HELIX 10 AB1 SER A 190 LEU A 197 1 8 HELIX 11 AB2 VAL A 205 VAL A 209 5 5 HELIX 12 AB3 ALA A 210 GLY A 224 1 15 HELIX 13 AB4 HIS A 225 LEU A 243 1 19 HELIX 14 AB5 PRO A 249 LEU A 259 1 11 HELIX 15 AB6 THR A 275 ALA A 289 1 15 HELIX 16 AB7 CYS B 20 GLY B 35 1 16 HELIX 17 AB8 GLU B 47 LEU B 51 5 5 HELIX 18 AB9 ASN B 52 ASP B 68 1 17 HELIX 19 AC1 ALA B 81 ARG B 91 1 11 HELIX 20 AC2 SER B 111 HIS B 125 1 15 HELIX 21 AC3 VAL B 135 GLY B 140 1 6 HELIX 22 AC4 LEU B 144 LYS B 153 1 10 HELIX 23 AC5 THR B 168 GLU B 175 1 8 HELIX 24 AC6 ASP B 187 ALA B 189 5 3 HELIX 25 AC7 SER B 190 LEU B 197 1 8 HELIX 26 AC8 VAL B 205 VAL B 209 5 5 HELIX 27 AC9 ALA B 210 GLU B 223 1 14 HELIX 28 AD1 HIS B 225 LEU B 243 1 19 HELIX 29 AD2 PRO B 249 LEU B 259 1 11 HELIX 30 AD3 THR B 275 ALA B 289 1 15 SHEET 1 AA1 9 GLY A 4 ALA A 8 0 SHEET 2 AA1 9 ALA A 38 SER A 41 1 O VAL A 40 N VAL A 7 SHEET 3 AA1 9 VAL A 73 GLY A 76 1 O ILE A 74 N ILE A 39 SHEET 4 AA1 9 GLY A 99 VAL A 103 1 O LEU A 101 N ALA A 75 SHEET 5 AA1 9 GLN A 130 ASN A 134 1 O ILE A 131 N CYS A 100 SHEET 6 AA1 9 ILE A 157 GLU A 162 1 O VPV A 161 N LEU A 132 SHEET 7 AA1 9 VAL A 182 SER A 185 1 O LEU A 184 N GLU A 162 SHEET 8 AA1 9 GLY A 201 SER A 204 1 O ILE A 203 N SER A 185 SHEET 9 AA1 9 GLY A 4 ALA A 8 1 N ILE A 6 O SER A 204 SHEET 1 AA2 9 GLY B 4 ALA B 8 0 SHEET 2 AA2 9 ALA B 38 SER B 41 1 O VAL B 40 N VAL B 7 SHEET 3 AA2 9 VAL B 73 GLY B 76 1 O ILE B 74 N ILE B 39 SHEET 4 AA2 9 GLY B 99 VAL B 103 1 O LEU B 101 N ALA B 75 SHEET 5 AA2 9 GLN B 130 ASN B 134 1 O ILE B 131 N CYS B 100 SHEET 6 AA2 9 ILE B 157 GLU B 162 1 O VPV B 161 N LEU B 132 SHEET 7 AA2 9 VAL B 182 SER B 185 1 O LEU B 184 N GLU B 162 SHEET 8 AA2 9 GLY B 201 SER B 204 1 O ILE B 203 N SER B 185 SHEET 9 AA2 9 GLY B 4 ALA B 8 1 N ILE B 6 O SER B 204 LINK C ILE A 160 N VPV A 161 1555 1555 1.52 LINK C VPV A 161 N GLU A 162 1555 1555 1.49 LINK C ILE B 160 N VPV B 161 1555 1555 1.38 LINK C VPV B 161 N GLU B 162 1555 1555 1.45 LINK OD1 ASN A 80 K K A 302 1555 1555 2.60 LINK OE2 GLU A 84 K K A 302 1555 1555 2.69 LINK O ALA A 152 K K A 301 1555 1555 2.73 LINK O VAL A 154 K K A 301 1555 1555 2.63 LINK O LYS A 155 K K A 301 1555 1555 3.08 LINK O ILE A 157 K K A 301 1555 1555 2.62 LINK K K A 301 O HOH A 617 1555 1555 2.71 LINK K K A 301 O HOH A 646 1555 1555 2.78 LINK K K A 302 O HOH A 608 1555 1555 3.02 LINK K K A 302 O ALA B 49 1555 1555 2.63 LINK K K A 302 O3 GOL B 302 1555 1555 2.85 LINK K K A 302 O HOH B 479 1555 1555 2.91 LINK K K A 302 O HOH B 533 1555 1555 3.29 LINK O ALA B 152 K K B 301 1555 1555 2.65 LINK O VAL B 154 K K B 301 1555 1555 2.68 LINK O LYS B 155 K K B 301 1555 1555 3.21 LINK O ILE B 157 K K B 301 1555 1555 2.63 LINK K K B 301 O HOH B 645 1555 1555 2.89 LINK K K B 301 O HOH B 665 1555 1555 2.67 CISPEP 1 ASN A 248 PRO A 249 0 6.71 CISPEP 2 LEU A 269 PRO A 270 0 19.40 CISPEP 3 ASN B 248 PRO B 249 0 15.69 CISPEP 4 LEU B 269 PRO B 270 0 16.12 CRYST1 120.919 120.919 110.081 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 0.008270 0.004775 0.000000 0.00000 SCALE2 0.000000 0.009549 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009084 0.00000